Query 046450
Match_columns 392
No_of_seqs 220 out of 1267
Neff 8.2
Searched_HMMs 46136
Date Fri Mar 29 12:14:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046450.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046450hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03196 MOC1-like protein; Pr 100.0 7.1E-56 1.5E-60 447.6 22.9 313 47-367 96-448 (487)
2 PF02536 mTERF: mTERF; InterP 100.0 1.9E-48 4.1E-53 381.7 5.4 304 50-356 3-345 (345)
3 PLN03196 MOC1-like protein; Pr 100.0 1.8E-43 3.9E-48 357.4 18.1 302 45-358 65-412 (487)
4 PF02536 mTERF: mTERF; InterP 100.0 1.1E-36 2.3E-41 298.6 2.6 272 81-357 2-314 (345)
5 KOG1267 Mitochondrial transcri 99.9 1.3E-27 2.8E-32 239.4 14.1 285 44-334 59-411 (413)
6 KOG1267 Mitochondrial transcri 99.7 6.5E-18 1.4E-22 169.4 11.9 210 111-326 90-334 (413)
7 smart00733 Mterf Mitochondrial 97.2 0.00035 7.5E-09 42.5 2.7 30 272-302 2-31 (31)
8 smart00733 Mterf Mitochondrial 96.8 0.00064 1.4E-08 41.2 1.8 28 168-196 3-30 (31)
9 PF11955 PORR: Plant organelle 92.5 0.73 1.6E-05 45.0 9.1 226 83-312 44-317 (335)
10 cd04790 HTH_Cfa-like_unk Helix 90.2 0.45 9.7E-06 41.9 4.6 48 220-273 119-167 (172)
11 cd04790 HTH_Cfa-like_unk Helix 74.1 6.2 0.00013 34.7 4.9 24 78-101 49-72 (172)
12 PF04695 Pex14_N: Peroxisomal 70.9 7.6 0.00016 32.7 4.6 31 251-281 21-51 (136)
13 PF04695 Pex14_N: Peroxisomal 70.2 5.6 0.00012 33.5 3.6 27 112-138 23-49 (136)
14 PF11955 PORR: Plant organelle 66.9 27 0.00059 34.1 8.1 33 253-285 119-152 (335)
15 COG1125 OpuBA ABC-type proline 59.5 21 0.00045 33.7 5.4 66 249-314 69-137 (309)
16 PF00627 UBA: UBA/TS-N domain; 58.0 16 0.00036 23.0 3.3 23 255-277 4-26 (37)
17 smart00165 UBA Ubiquitin assoc 55.6 20 0.00044 22.4 3.4 23 255-277 3-25 (37)
18 PF11181 YflT: Heat induced st 55.6 46 0.001 26.3 6.3 79 181-272 9-89 (103)
19 PRK14136 recX recombination re 52.8 2.1E+02 0.0046 27.6 11.1 106 147-277 195-302 (309)
20 cd00194 UBA Ubiquitin Associat 52.5 24 0.00052 22.1 3.4 23 255-277 3-25 (38)
21 PRK11613 folP dihydropteroate 47.6 71 0.0015 30.4 7.2 70 287-364 164-233 (282)
22 KOG0011 Nucleotide excision re 47.5 12 0.00025 36.1 1.8 105 53-174 144-262 (340)
23 PF02022 Integrase_Zn: Integra 45.6 41 0.00089 21.9 3.6 29 252-280 7-36 (40)
24 PF14490 HHH_4: Helix-hairpin- 45.5 62 0.0014 25.1 5.5 36 95-130 38-74 (94)
25 PF07499 RuvA_C: RuvA, C-termi 45.1 43 0.00092 22.4 3.9 25 253-277 3-27 (47)
26 TIGR01448 recD_rel helicase, p 44.7 47 0.001 36.1 6.2 93 46-144 80-186 (720)
27 PF11212 DUF2999: Protein of u 44.6 43 0.00093 24.8 3.9 56 77-140 2-60 (82)
28 PF00356 LacI: Bacterial regul 41.6 44 0.00095 22.4 3.4 41 191-234 6-46 (46)
29 PF03960 ArsC: ArsC family; I 36.7 40 0.00086 26.9 3.2 20 124-143 71-90 (110)
30 PF08671 SinI: Anti-repressor 33.3 67 0.0015 19.6 2.9 24 253-276 5-28 (30)
31 PRK08561 rps15p 30S ribosomal 33.1 93 0.002 26.7 4.9 114 206-341 20-139 (151)
32 COG3620 Predicted transcriptio 33.1 67 0.0014 28.0 4.0 20 264-283 146-165 (187)
33 PF02787 CPSase_L_D3: Carbamoy 32.2 83 0.0018 26.0 4.4 70 184-274 13-82 (123)
34 PRK00116 ruvA Holliday junctio 32.1 58 0.0013 29.0 3.8 25 148-172 149-173 (192)
35 TIGR01448 recD_rel helicase, p 32.0 1.1E+02 0.0024 33.3 6.5 99 72-180 73-186 (720)
36 PRK14487 cbb3-type cytochrome 31.3 1.3E+02 0.0029 27.4 5.8 63 204-266 134-209 (217)
37 PF14490 HHH_4: Helix-hairpin- 30.8 1.3E+02 0.0028 23.3 5.1 20 78-97 10-29 (94)
38 PF02631 RecX: RecX family; I 29.8 3E+02 0.0064 22.2 8.3 107 148-276 11-118 (121)
39 PF08069 Ribosomal_S13_N: Ribo 29.4 19 0.00041 25.8 0.1 35 242-276 22-56 (60)
40 PHA02591 hypothetical protein; 28.7 81 0.0018 23.8 3.3 44 54-97 22-69 (83)
41 PF13331 DUF4093: Domain of un 26.5 2.7E+02 0.0058 21.5 6.1 22 112-133 65-86 (87)
42 smart00354 HTH_LACI helix_turn 26.0 1.1E+02 0.0025 22.1 3.9 40 192-234 8-47 (70)
43 PF11212 DUF2999: Protein of u 25.6 1.1E+02 0.0024 22.7 3.5 49 149-205 2-50 (82)
44 cd08319 Death_RAIDD Death doma 24.6 3.1E+02 0.0068 20.9 6.1 37 81-121 18-54 (83)
45 cd00739 DHPS DHPS subgroup of 24.4 2.5E+02 0.0053 26.3 6.7 69 288-365 152-221 (257)
46 PF12244 DUF3606: Protein of u 24.3 52 0.0011 23.2 1.6 29 40-68 16-44 (57)
47 cd08319 Death_RAIDD Death doma 23.9 2.5E+02 0.0054 21.4 5.4 68 112-202 12-80 (83)
48 PF09278 MerR-DNA-bind: MerR, 23.7 79 0.0017 22.3 2.6 18 257-274 7-24 (65)
49 KOG0400 40S ribosomal protein 22.8 91 0.002 26.0 2.9 36 170-206 20-55 (151)
50 PRK00116 ruvA Holliday junctio 22.6 1.4E+02 0.003 26.6 4.4 26 112-137 149-174 (192)
51 cd08306 Death_FADD Fas-associa 22.2 1.5E+02 0.0032 22.6 4.0 37 80-120 17-53 (86)
52 TIGR03060 PS_II_psb29 photosys 21.5 2.8E+02 0.006 25.3 6.1 42 46-87 76-118 (214)
53 cd01392 HTH_LacI Helix-turn-he 21.2 1.4E+02 0.003 19.8 3.3 40 192-234 5-44 (52)
54 PF10440 WIYLD: Ubiquitin-bind 20.9 1.8E+02 0.004 21.2 3.9 35 250-284 8-42 (65)
55 PF03960 ArsC: ArsC family; I 20.7 86 0.0019 24.9 2.5 54 55-108 32-91 (110)
56 cd04784 HTH_CadR-PbrR Helix-Tu 20.4 2.7E+02 0.0058 22.7 5.5 22 255-276 48-69 (127)
57 COG3620 Predicted transcriptio 20.3 97 0.0021 27.0 2.7 28 274-302 70-97 (187)
58 cd04768 HTH_BmrR-like Helix-Tu 20.3 2.1E+02 0.0045 22.2 4.5 24 255-278 48-71 (96)
59 KOG0400 40S ribosomal protein 20.1 88 0.0019 26.1 2.3 68 235-303 15-82 (151)
60 cd04788 HTH_NolA-AlbR Helix-Tu 20.1 2.9E+02 0.0062 21.4 5.3 24 255-278 48-71 (96)
No 1
>PLN03196 MOC1-like protein; Provisional
Probab=100.00 E-value=7.1e-56 Score=447.60 Aligned_cols=313 Identities=21% Similarity=0.386 Sum_probs=231.5
Q ss_pred HHHhHhhcCCCHHHHHhhcccc-cccCCCChhhHHHhhhhCCCChHHHHHHHHhCCceeccCcCCchhHHHHHHHhCCCC
Q 046450 47 VSFLTHSCGLSLEKAISVSKLV-KIQDTEKPNSSIQLLTSRGFTKPQIATLISKYPRILSHDPEKVLKPKIEYLESLGIS 125 (392)
Q Consensus 47 v~~L~~~~Gls~~~~~~i~~~~-~~~~~~~~~~~l~~L~~lGl~~~~i~~ll~~~P~lL~~~~~~~l~p~v~fL~~lGls 125 (392)
++|| .++|++.+++.+ .+.+ .+....++.++++||+++|+++.++++++.++|.+|.+++++++.|+++||+++|++
T Consensus 96 l~~L-~s~G~~~~~i~~-~P~iL~~~v~~~l~Pvl~fL~~lG~s~~~i~~lI~~~P~lL~~sve~~L~P~v~fL~~lGvs 173 (487)
T PLN03196 96 VEFL-HKLGLTIEDINE-YPLVLGCSVKKNMIPVLDYLEKLGVTRSSLPELLRRYPQVLHASVVVDLAPVVKYLQGLDVK 173 (487)
T ss_pred HHHH-HHcCCChHHhcc-CcHHhhcCHhhhhHHHHHHHHHcCCCHHHHHHHHHhCCceecccHHHHHHHHHHHHHHcCCC
Confidence 3555 466666666652 1222 222234566666666666666666666666666666666666666666666666666
Q ss_pred chhHHHhhhcCccccccccccchhhHHHHHHhhccCCchHHHHHhhCcceeccCcccchhhhHHHHHHCCCCchhhhccc
Q 046450 126 GPDLAKILCPYPELLSRSLENHIIPTFDFLKGVFQANGNLVYALKQSIRVVNSDIQKRVVPNMNTLRAHGVPEPHIARLI 205 (392)
Q Consensus 126 ~~~l~~il~~~P~lL~~~~~~~l~p~v~fL~~lg~~~~~i~~il~~~P~lL~~s~~~~l~~~v~~L~~lGv~~~~i~~ll 205 (392)
++++++++.++|++|++++++++.|+++||+++|++.+++++++.++|++|+++++++++|+++||+++|++.++|++++
T Consensus 174 ~~~i~~~l~r~P~LL~~~~e~~l~p~v~fL~~lGvs~~~i~~il~~~P~iL~~sve~~i~P~v~fL~~lGv~~~~I~~il 253 (487)
T PLN03196 174 RQDIPRVLERYPELLGFKLEGTMSTSVAYLVSIGVAPRDIGPMLTRFPEILGMRVGNNIKPKVDYLESLGLPRLAVARIL 253 (487)
T ss_pred HHHHHHHHHhCchhhcCCHHHHHHHHHHHHHHcCCCHHHHHHHHHhCcHHhhcChhhhHHHHHHHHHHcCCCHHHHHHHH
Confidence 66666666666666666666666666666666666666666666666666666666666666666666666666666666
Q ss_pred ccCCceeeechh-hHHHHHHHHHHhCCCCC-------------------------------------chh-HHHHHHHHH
Q 046450 206 MLQPPSLVLRAE-LFKNVVDVIKEMGFEPS-------------------------------------SKS-FILAVRSMA 246 (392)
Q Consensus 206 ~~~P~il~~~~~-~~~~~v~~L~~lG~~~~-------------------------------------~~~-~~~~~~~~~ 246 (392)
.++|++|+++.+ ++++++++|.++|++++ +.. ++...+.++
T Consensus 254 ~~~P~iL~~sle~~lkp~v~~L~elGv~~~~i~~lI~~~P~iL~~s~e~kl~~~~~fL~~~lG~s~e~i~~~v~k~P~il 333 (487)
T PLN03196 254 EKRPYILGFDLEETVKPNVECLLEFGVRKEALPSVIAQYPDILGLDLKAKLAEQQYWLTSKLKIDPEDFGRVIEKLPQIV 333 (487)
T ss_pred HhCCceeEcCHHHhHHHHHHHHHHcCCCHHHHHHHHHhCCceeEecHHHhhhHHHHHHHHhhCCCHHHHHHHHHhcchhh
Confidence 666666666654 56666666666666554 221 222334556
Q ss_pred hcCHHHHHHHHHHHHHcCCCHHHHHHHHHhCCccccccHHHHHHHHHHHHHhhCCChhhHhcCCcccccCCCCccchhHH
Q 046450 247 MSSKATWQRKKEILISFGWSEDEFRMVFKRQPLFMMASAKKIRKLMDFFVNKIGLEPSDIARYPNLLIGSLEKKVLPRWS 326 (392)
Q Consensus 247 ~~s~~~l~~kv~fL~~lG~s~~ei~~~i~~~P~iL~~s~e~L~~~~~fL~~~~G~~~~~i~~~P~lL~~sle~~l~pR~~ 326 (392)
.+++++|++|++||+++||+.++|.+|+.++|++|++|.++|+++++||+++||++.++|++||++|+||+|+||+|||+
T Consensus 334 ~lSe~kl~~kvefL~~~Gls~edI~~mv~k~P~lL~~S~~~l~~k~dFlvneMg~~~~~Iv~fP~~LsySLEkRI~PR~~ 413 (487)
T PLN03196 334 SLNRNVALKHVEFLRGRGFSAQDVAKMVVRCPQILALNLEIMKPSLEFFKKEMKRPLKELVEFPAYFTYGLESRIKPRYE 413 (487)
T ss_pred cccHHHHHHHHHHHHHcCCCHHHHHHHHHhCCceeeccHHHHHHHHHHHHHHhCCCHHHHHhChHHhccChhhhhHHHHH
Confidence 78899999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred HHHHHHHcCCCCCCcccccccccChHHHHHHHhccCCCChH
Q 046450 327 VLQVLMSKNLLKKDVNVSLALFVTKEVFERRFVTSYMHEPE 367 (392)
Q Consensus 327 ~l~~L~~~G~~~~~~~l~~~l~~s~~~F~~~~v~~~~e~~~ 367 (392)
+ |+++|+ ..++.++|.+||++|+++|+..|.|.++
T Consensus 414 ~---L~~kGl---~~sL~~~L~~sd~~F~~r~v~~y~e~~~ 448 (487)
T PLN03196 414 R---VAKKGI---KCSLAWFLNCSDDKFEQRMSGDFIEGEE 448 (487)
T ss_pred H---HHHcCC---CCCHHHHhccCHHHHHHHHhhhcccccc
Confidence 6 779998 6799999999999999999999998733
No 2
>PF02536 mTERF: mTERF; InterPro: IPR003690 This family currently contains one sequence of known function human mitochondrial transcription termination factor (mTERF), a multizipper protein but binds to DNA as a monomer, with evidence pointing to intramolecular leucine zipper interactions []. The precursors contain a mitochondrial targeting sequence, and the mature mTERF exhibits three leucine zippers, of which one is bipartite, and two widely spaced basic domains. Both basic domains and the three leucine zipper motifs are necessary for DNA binding. The leucine zippers are not implicated in a dimerisation role as in other leucine zippers []. The rest of the family consists of hypothetical proteins none of which have any functional information.; PDB: 3M66_A 3OPG_A 3MVA_O 3MVB_O 3N7Q_A 3N6S_A.
Probab=100.00 E-value=1.9e-48 Score=381.71 Aligned_cols=304 Identities=28% Similarity=0.447 Sum_probs=215.0
Q ss_pred hHhhcCCCHHHHHhhcccc----cccCCCChhhHHHhhhhCCCChHHHHHHHHhCCceeccCcCCchhHHHHHHHhCCCC
Q 046450 50 LTHSCGLSLEKAISVSKLV----KIQDTEKPNSSIQLLTSRGFTKPQIATLISKYPRILSHDPEKVLKPKIEYLESLGIS 125 (392)
Q Consensus 50 L~~~~Gls~~~~~~i~~~~----~~~~~~~~~~~l~~L~~lGl~~~~i~~ll~~~P~lL~~~~~~~l~p~v~fL~~lGls 125 (392)
+.+++||+.+++.+++++. ..+...++.++++||.++|++..++++++.++|++|.++.++++.|.++||.++|++
T Consensus 3 ~~~~~gf~~~~i~~~i~~~P~~l~~~~~~~l~pk~~fl~s~G~s~~~i~~il~~~P~il~~s~~~~i~p~~~~L~~~~~s 82 (345)
T PF02536_consen 3 LLKNHGFSDSQISKLIRRYPRLLLCDPEKTLLPKLEFLRSLGFSSSDIAKILSKNPQILSRSLEKNIIPVFDFLKSIGLS 82 (345)
T ss_dssp HHHHHHHHTS-HHHHHH-H-HHHHT-SS-HHHHHHHHHHHTT--HHHHHHHHHH-GGGGGS--HHHHHHHHHHHTTTSS-
T ss_pred HHHHcCCCHHHHHHHHHhCCceEEecCccchhHHHHHHHHCCCCHHHHHHHHHhChHHHhccchhhHHHHHHHHHHHcCC
Confidence 3467788888888887653 234446778888888888888888888888888888888777788888888888888
Q ss_pred chhHHHhhhcCccccccccccchhhHHHHHHhhccCCchHHHHHhhCcceeccCcccchhhhHHHHHHCCCCchhhhccc
Q 046450 126 GPDLAKILCPYPELLSRSLENHIIPTFDFLKGVFQANGNLVYALKQSIRVVNSDIQKRVVPNMNTLRAHGVPEPHIARLI 205 (392)
Q Consensus 126 ~~~l~~il~~~P~lL~~~~~~~l~p~v~fL~~lg~~~~~i~~il~~~P~lL~~s~~~~l~~~v~~L~~lGv~~~~i~~ll 205 (392)
++++.+++.++|++|..+.+.++.+++.||+++|++.+.+.+.+..+|.++... +++++.++++.++|++++++.+++
T Consensus 83 ~~d~~~~l~r~p~~l~~~~~~~l~~~v~~L~~lGv~~~~~~~~l~~~~~~~~~~--~~~~~~v~~l~~lG~~~~~~~~vi 160 (345)
T PF02536_consen 83 DEDIVKVLKRYPRILSFSVEENLSPNVAFLRSLGVPPSQIISLLISRPPLFLSS--EKIKERVEFLKELGFDPEKIGRVI 160 (345)
T ss_dssp HHHHHHHHHH-SHHHHS---HHHHHHHHHHHHTT--HHHHHHHHHH-CHHHHS---HHHHCHHHHHCCCTSSHHHHCCCH
T ss_pred HHHHHHHHHhcchhhccchHhhhhhhhhHHhhcCCcHHHHHHHHHhcCccccch--hHHHHHHHHHHHhCCCchhhcccc
Confidence 888888888888888777666788888888888887776666666666655444 347777777777777777777777
Q ss_pred ccCCceeeec-hhhHHHHHHHHHHhCCCCCch----------------------------------hHHHHHHHHHhcCH
Q 046450 206 MLQPPSLVLR-AELFKNVVDVIKEMGFEPSSK----------------------------------SFILAVRSMAMSSK 250 (392)
Q Consensus 206 ~~~P~il~~~-~~~~~~~v~~L~~lG~~~~~~----------------------------------~~~~~~~~~~~~s~ 250 (392)
..+|.++... .+.+++++++|+++|++.++. .++...+.++.++.
T Consensus 161 ~~~P~~l~~~~~~~~~~~v~~L~~~G~~~~~i~~~l~~~P~~l~~s~~~~l~~~~~l~~~~~~~~~~~i~~~p~il~~~~ 240 (345)
T PF02536_consen 161 AKNPRLLLSDSESELKPKVEFLRSLGFSKEDIGKLLRKCPRLLSLSVEKILEPVLYLLSSGGVEEERVIKKFPQILSLSE 240 (345)
T ss_dssp HHHHHHHCGSCCCCCHHHHHHHHHCTT-GHHHHHHHHHTTTGGGCGCHC---------------------------THHH
T ss_pred cccchhhccccHHHHHHHHHHHHhhcccchhhhHHhhcccceecccccccccccccccccccccccccccccccccccch
Confidence 7777444433 345677777777777665532 12222233445567
Q ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHhCCccccccHHHHHHHHHHHHHhhCCChhhHhcCCcccccCCCCccchhHHHHHH
Q 046450 251 ATWQRKKEILISFGWSEDEFRMVFKRQPLFMMASAKKIRKLMDFFVNKIGLEPSDIARYPNLLIGSLEKKVLPRWSVLQV 330 (392)
Q Consensus 251 ~~l~~kv~fL~~lG~s~~ei~~~i~~~P~iL~~s~e~L~~~~~fL~~~~G~~~~~i~~~P~lL~~sle~~l~pR~~~l~~ 330 (392)
+++.++++||+++|||.+||.+|+.++|+||++|.++++++++||.++||++.++|+++|++|+||+|+||+|||+++++
T Consensus 241 ~~l~~~i~~L~~lG~s~~ei~~mv~~~P~iL~~s~e~l~~k~~fl~~~m~~~~~~i~~~P~~l~~sLe~ri~PR~~~~~~ 320 (345)
T PF02536_consen 241 EKLKPKIEFLQSLGFSEEEIAKMVRRFPQILSYSIEKLKPKFEFLVKEMGLPLEEIVEFPQYLSYSLEKRIKPRYEVLKV 320 (345)
T ss_dssp HHHHHHHHHHHTTT--HHHHHHHHHHSGGGGGS-HHHHHHHHHHHHHCCT--HHHHHHSCHHHCS-HHHHHHHHHHHHHT
T ss_pred HhHHHHHHHHHHhcCcHHHHHHHHHhCcchhhcchhhhhHHHHHHHHHhCcCHHHHhhCCceeEechhhhhhhHHHHHHH
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHcCCCCCCcccccccccChHHHHH
Q 046450 331 LMSKNLLKKDVNVSLALFVTKEVFER 356 (392)
Q Consensus 331 L~~~G~~~~~~~l~~~l~~s~~~F~~ 356 (392)
|+++|. ..++++.+++.+||++|++
T Consensus 321 l~~~g~-~~~~sl~~~l~~s~~~F~~ 345 (345)
T PF02536_consen 321 LKSKGL-IINPSLSSMLSCSDEEFLK 345 (345)
T ss_dssp T--TTT-GGGGGS-HHHHHHHHHHT-
T ss_pred HHHCcC-CCCCCHHHHhhccHHHhcC
Confidence 999997 5689999999999999964
No 3
>PLN03196 MOC1-like protein; Provisional
Probab=100.00 E-value=1.8e-43 Score=357.40 Aligned_cols=302 Identities=19% Similarity=0.306 Sum_probs=248.5
Q ss_pred chHHHhHhhcCCCHHHHHhhcccccccCCCChhhHHHhhhhCCCChHHHHHHHHhCCceeccCcCCchhHHHHHHHhCCC
Q 046450 45 PTVSFLTHSCGLSLEKAISVSKLVKIQDTEKPNSSIQLLTSRGFTKPQIATLISKYPRILSHDPEKVLKPKIEYLESLGI 124 (392)
Q Consensus 45 ~~v~~L~~~~Gls~~~~~~i~~~~~~~~~~~~~~~l~~L~~lGl~~~~i~~ll~~~P~lL~~~~~~~l~p~v~fL~~lGl 124 (392)
..++|| .++|++..++.++.. + .+.+.+.++++||+++|++++||. ++|++|++++++++.|+++||.++|+
T Consensus 65 ~~~~~L-~~lgi~~~~l~~~~~--p-~~~~~~~~~l~~L~s~G~~~~~i~----~~P~iL~~~v~~~l~Pvl~fL~~lG~ 136 (487)
T PLN03196 65 KVLDFL-RGIGIDPDELDGLEL--P-STVDVMRERVEFLHKLGLTIEDIN----EYPLVLGCSVKKNMIPVLDYLEKLGV 136 (487)
T ss_pred HHHHHH-HHcCCCchhhhccCC--C-ccHHHHHHHHHHHHHcCCChHHhc----cCcHHhhcCHhhhhHHHHHHHHHcCC
Confidence 356999 689999999987542 1 334678899999999999999997 79999999999999999999999999
Q ss_pred CchhHHHhhhcCccccccccccchhhHHHHHHhhccCCchHHHHHhhCcceeccCcccchhhhHHHHHHCCCCchhhhcc
Q 046450 125 SGPDLAKILCPYPELLSRSLENHIIPTFDFLKGVFQANGNLVYALKQSIRVVNSDIQKRVVPNMNTLRAHGVPEPHIARL 204 (392)
Q Consensus 125 s~~~l~~il~~~P~lL~~~~~~~l~p~v~fL~~lg~~~~~i~~il~~~P~lL~~s~~~~l~~~v~~L~~lGv~~~~i~~l 204 (392)
+..+|+++|.++|.+|..++++++.|+++||+++|+++++|.+++.++|++|++++++++.++++||+++|+++++|+++
T Consensus 137 s~~~i~~lI~~~P~lL~~sve~~L~P~v~fL~~lGvs~~~i~~~l~r~P~LL~~~~e~~l~p~v~fL~~lGvs~~~i~~i 216 (487)
T PLN03196 137 TRSSLPELLRRYPQVLHASVVVDLAPVVKYLQGLDVKRQDIPRVLERYPELLGFKLEGTMSTSVAYLVSIGVAPRDIGPM 216 (487)
T ss_pred CHHHHHHHHHhCCceecccHHHHHHHHHHHHHHcCCCHHHHHHHHHhCchhhcCCHHHHHHHHHHHHHHcCCCHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCCceeeechh-hHHHHHHHHHHhCCCCCchh--HHHHHHHHH-----------------------------------
Q 046450 205 IMLQPPSLVLRAE-LFKNVVDVIKEMGFEPSSKS--FILAVRSMA----------------------------------- 246 (392)
Q Consensus 205 l~~~P~il~~~~~-~~~~~v~~L~~lG~~~~~~~--~~~~~~~~~----------------------------------- 246 (392)
+.++|++|+.+.+ +++++++||.++|++.+... +.+.|.++.
T Consensus 217 l~~~P~iL~~sve~~i~P~v~fL~~lGv~~~~I~~il~~~P~iL~~sle~~lkp~v~~L~elGv~~~~i~~lI~~~P~iL 296 (487)
T PLN03196 217 LTRFPEILGMRVGNNIKPKVDYLESLGLPRLAVARILEKRPYILGFDLEETVKPNVECLLEFGVRKEALPSVIAQYPDIL 296 (487)
T ss_pred HHhCcHHhhcChhhhHHHHHHHHHHcCCCHHHHHHHHHhCCceeEcCHHHhHHHHHHHHHHcCCCHHHHHHHHHhCCcee
Confidence 9999999999976 69999999999999887431 222222111
Q ss_pred hc-CHHHHHHHHHHHH-HcCCCHHHHHHHHHhCCccccccHHHHHHHHHHHHHhhCCChhhH----hcCCcccccCCCCc
Q 046450 247 MS-SKATWQRKKEILI-SFGWSEDEFRMVFKRQPLFMMASAKKIRKLMDFFVNKIGLEPSDI----ARYPNLLIGSLEKK 320 (392)
Q Consensus 247 ~~-s~~~l~~kv~fL~-~lG~s~~ei~~~i~~~P~iL~~s~e~L~~~~~fL~~~~G~~~~~i----~~~P~lL~~sle~~ 320 (392)
.. .++++.++++|+. ++|++.+++..++.++|+++++|.++++++++||.+ +|++.++| .++|++|+||.+ +
T Consensus 297 ~~s~e~kl~~~~~fL~~~lG~s~e~i~~~v~k~P~il~lSe~kl~~kvefL~~-~Gls~edI~~mv~k~P~lL~~S~~-~ 374 (487)
T PLN03196 297 GLDLKAKLAEQQYWLTSKLKIDPEDFGRVIEKLPQIVSLNRNVALKHVEFLRG-RGFSAQDVAKMVVRCPQILALNLE-I 374 (487)
T ss_pred EecHHHhhhHHHHHHHHhhCCCHHHHHHHHHhcchhhcccHHHHHHHHHHHHH-cCCCHHHHHHHHHhCCceeeccHH-H
Confidence 11 1345666667775 677777777777777888888888888889999987 89998887 589999999985 8
Q ss_pred cchhHHHHHHHHHcCCCCC-CcccccccccCh-HHHHHHH
Q 046450 321 VLPRWSVLQVLMSKNLLKK-DVNVSLALFVTK-EVFERRF 358 (392)
Q Consensus 321 l~pR~~~l~~L~~~G~~~~-~~~l~~~l~~s~-~~F~~~~ 358 (392)
|+++++|+ ..++|...+ -+....++++|= ++-..||
T Consensus 375 l~~k~dFl--vneMg~~~~~Iv~fP~~LsySLEkRI~PR~ 412 (487)
T PLN03196 375 MKPSLEFF--KKEMKRPLKELVEFPAYFTYGLESRIKPRY 412 (487)
T ss_pred HHHHHHHH--HHHhCCCHHHHHhChHHhccChhhhhHHHH
Confidence 99998874 345665322 244567777763 3444333
No 4
>PF02536 mTERF: mTERF; InterPro: IPR003690 This family currently contains one sequence of known function human mitochondrial transcription termination factor (mTERF), a multizipper protein but binds to DNA as a monomer, with evidence pointing to intramolecular leucine zipper interactions []. The precursors contain a mitochondrial targeting sequence, and the mature mTERF exhibits three leucine zippers, of which one is bipartite, and two widely spaced basic domains. Both basic domains and the three leucine zipper motifs are necessary for DNA binding. The leucine zippers are not implicated in a dimerisation role as in other leucine zippers []. The rest of the family consists of hypothetical proteins none of which have any functional information.; PDB: 3M66_A 3OPG_A 3MVA_O 3MVB_O 3N7Q_A 3N6S_A.
Probab=100.00 E-value=1.1e-36 Score=298.56 Aligned_cols=272 Identities=35% Similarity=0.626 Sum_probs=218.2
Q ss_pred HhhhhCCCChHHHHHHHHhCCceeccCcCCchhHHHHHHHhCCCCchhHHHhhhcCccccccccccchhhHHHHHHhhcc
Q 046450 81 QLLTSRGFTKPQIATLISKYPRILSHDPEKVLKPKIEYLESLGISGPDLAKILCPYPELLSRSLENHIIPTFDFLKGVFQ 160 (392)
Q Consensus 81 ~~L~~lGl~~~~i~~ll~~~P~lL~~~~~~~l~p~v~fL~~lGls~~~l~~il~~~P~lL~~~~~~~l~p~v~fL~~lg~ 160 (392)
++|+++|+++++|.++++++|.++.+++++++.|+++||.++|++..++++++.++|.+|..++++++.|.++||+++|.
T Consensus 2 ~~~~~~gf~~~~i~~~i~~~P~~l~~~~~~~l~pk~~fl~s~G~s~~~i~~il~~~P~il~~s~~~~i~p~~~~L~~~~~ 81 (345)
T PF02536_consen 2 DLLKNHGFSDSQISKLIRRYPRLLLCDPEKTLLPKLEFLRSLGFSSSDIAKILSKNPQILSRSLEKNIIPVFDFLKSIGL 81 (345)
T ss_dssp HHHHHHHHHTS-HHHHHH-H-HHHHT-SS-HHHHHHHHHHHTT--HHHHHHHHHH-GGGGGS--HHHHHHHHHHHTTTSS
T ss_pred hHHHHcCCCHHHHHHHHHhCCceEEecCccchhHHHHHHHHCCCCHHHHHHHHHhChHHHhccchhhHHHHHHHHHHHcC
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCchHHHHHhhCcceeccCcccchhhhHHHHHHCCCCchhhhcccccCCceeeechhhHHHHHHHHHHhCCCCCchh--H
Q 046450 161 ANGNLVYALKQSIRVVNSDIQKRVVPNMNTLRAHGVPEPHIARLIMLQPPSLVLRAELFKNVVDVIKEMGFEPSSKS--F 238 (392)
Q Consensus 161 ~~~~i~~il~~~P~lL~~s~~~~l~~~v~~L~~lGv~~~~i~~ll~~~P~il~~~~~~~~~~v~~L~~lG~~~~~~~--~ 238 (392)
+++++.+++.++|++|..+.+.++.+++++|+++|++++.+..++...|..+... +++++.++++.++|+++++.. .
T Consensus 82 s~~d~~~~l~r~p~~l~~~~~~~l~~~v~~L~~lGv~~~~~~~~l~~~~~~~~~~-~~~~~~v~~l~~lG~~~~~~~~vi 160 (345)
T PF02536_consen 82 SDEDIVKVLKRYPRILSFSVEENLSPNVAFLRSLGVPPSQIISLLISRPPLFLSS-EKIKERVEFLKELGFDPEKIGRVI 160 (345)
T ss_dssp -HHHHHHHHHH-SHHHHS---HHHHHHHHHHHHTT--HHHHHHHHHH-CHHHHS--HHHHCHHHHHCCCTSSHHHHCCCH
T ss_pred CHHHHHHHHHhcchhhccchHhhhhhhhhHHhhcCCcHHHHHHHHHhcCccccch-hHHHHHHHHHHHhCCCchhhcccc
Confidence 9999999999999999998887899999999999999998888888888876655 899999999999999998753 4
Q ss_pred HHHHHHHHhcCHHHHHHHHHHHHHcCCCHHHHHHHHHhCCccccccHHH-------------------------------
Q 046450 239 ILAVRSMAMSSKATWQRKKEILISFGWSEDEFRMVFKRQPLFMMASAKK------------------------------- 287 (392)
Q Consensus 239 ~~~~~~~~~~s~~~l~~kv~fL~~lG~s~~ei~~~i~~~P~iL~~s~e~------------------------------- 287 (392)
..+|..+...+++.|+++++||+++|++.+++.+++.++|.++.+|.++
T Consensus 161 ~~~P~~l~~~~~~~~~~~v~~L~~~G~~~~~i~~~l~~~P~~l~~s~~~~l~~~~~l~~~~~~~~~~~i~~~p~il~~~~ 240 (345)
T PF02536_consen 161 AKNPRLLLSDSESELKPKVEFLRSLGFSKEDIGKLLRKCPRLLSLSVEKILEPVLYLLSSGGVEEERVIKKFPQILSLSE 240 (345)
T ss_dssp HHHHHHHCGSCCCCCHHHHHHHHHCTT-GHHHHHHHHHTTTGGGCGCHC---------------------------THHH
T ss_pred cccchhhccccHHHHHHHHHHHHhhcccchhhhHHhhcccceecccccccccccccccccccccccccccccccccccch
Confidence 5667788888899999999999999999999999999999999988864
Q ss_pred --HHHHHHHHHHhhCCChhhH----hcCCcccccCCCCccchhHHHHHHHHHcCCCCCC-cccccccccChH-HHHHH
Q 046450 288 --IRKLMDFFVNKIGLEPSDI----ARYPNLLIGSLEKKVLPRWSVLQVLMSKNLLKKD-VNVSLALFVTKE-VFERR 357 (392)
Q Consensus 288 --L~~~~~fL~~~~G~~~~~i----~~~P~lL~~sle~~l~pR~~~l~~L~~~G~~~~~-~~l~~~l~~s~~-~F~~~ 357 (392)
+.++++||.+ +|++.++| .++|++|++|.++ ++++++|+ ..+.|+..++ ...+.++++|=+ +-..|
T Consensus 241 ~~l~~~i~~L~~-lG~s~~ei~~mv~~~P~iL~~s~e~-l~~k~~fl--~~~m~~~~~~i~~~P~~l~~sLe~ri~PR 314 (345)
T PF02536_consen 241 EKLKPKIEFLQS-LGFSEEEIAKMVRRFPQILSYSIEK-LKPKFEFL--VKEMGLPLEEIVEFPQYLSYSLEKRIKPR 314 (345)
T ss_dssp HHHHHHHHHHHT-TT--HHHHHHHHHHSGGGGGS-HHH-HHHHHHHH--HHCCT--HHHHHHSCHHHCS-HHHHHHHH
T ss_pred HhHHHHHHHHHH-hcCcHHHHHHHHHhCcchhhcchhh-hhHHHHHH--HHHhCcCHHHHhhCCceeEechhhhhhhH
Confidence 8889999998 99999887 5899999999995 99998874 3456774322 335677777763 34444
No 5
>KOG1267 consensus Mitochondrial transcription termination factor, mTERF [Transcription; General function prediction only]
Probab=99.95 E-value=1.3e-27 Score=239.36 Aligned_cols=285 Identities=25% Similarity=0.395 Sum_probs=247.4
Q ss_pred CchHHHhHhhcCCCHHHHHhhcccccccCCCChhhHHHhhhhCCCChHHHHHHHHhCCceeccCcCCchhHHHHHHHhCC
Q 046450 44 SPTVSFLTHSCGLSLEKAISVSKLVKIQDTEKPNSSIQLLTSRGFTKPQIATLISKYPRILSHDPEKVLKPKIEYLESLG 123 (392)
Q Consensus 44 ~~~v~~L~~~~Gls~~~~~~i~~~~~~~~~~~~~~~l~~L~~lGl~~~~i~~ll~~~P~lL~~~~~~~l~p~v~fL~~lG 123 (392)
.+++.|+++++|.+...+..+.+.+......++++++++|+++|+++.++..++..+|.++..+.++.+.|+..+|.+.|
T Consensus 59 ~f~~s~~~~s~~~~~~~~~~~~~~~~~~~~~~p~s~~~~l~s~g~~~~~i~s~i~~~p~ll~~~~~~~l~~~~~~l~~~g 138 (413)
T KOG1267|consen 59 NFESSYLVDSLGLSIKLARKLSREVSSEDSVNPSSVLSSLRSLGFTDSQISSIILSSPKLLYLSSENILKPKLRLLDSLG 138 (413)
T ss_pred CcceeeeccccccchhhHHHHHHHHHhhhccCcHHHHHHHHhcCCchhhcccccccCchhhhccchhhhhhhhhhhhccC
Confidence 57889999999999999999988877777789999999999999999999999999999999999999999999999999
Q ss_pred CCchhHHHhhhcCccccccccccchhhHHHHHHhhc-----------------------------------cCCchHHH-
Q 046450 124 ISGPDLAKILCPYPELLSRSLENHIIPTFDFLKGVF-----------------------------------QANGNLVY- 167 (392)
Q Consensus 124 ls~~~l~~il~~~P~lL~~~~~~~l~p~v~fL~~lg-----------------------------------~~~~~i~~- 167 (392)
++..++.+++...|.+|+.+.+.++.+.++|+++++ ...+++..
T Consensus 139 ~~~s~l~~i~s~~~~il~~~~~~~~~~~~~~l~~~~~~~~~s~~~~~~~~~~~~~~~~~~v~~~~~~~~lg~~~~~L~~~ 218 (413)
T KOG1267|consen 139 LPSSELSSIVSVVPKILLKSKGESLSTFIEFLKSIPPELLSSVVERLLTPVPSFLLNENSVERLDIRRELGVKPRLLKSL 218 (413)
T ss_pred ccccccchhhhccHHHHHhhcCCchhhHHHHhhccchhhhhhHHHHhccccccccccccccccchhhHHhCCCHHHHHHH
Confidence 999999999999999988777777888888888753 22222222
Q ss_pred -------------------------------HHhhCcceeccCcccchhhhHHHHHHCCCCchhhhcccccCCceeeech
Q 046450 168 -------------------------------ALKQSIRVVNSDIQKRVVPNMNTLRAHGVPEPHIARLIMLQPPSLVLRA 216 (392)
Q Consensus 168 -------------------------------il~~~P~lL~~s~~~~l~~~v~~L~~lGv~~~~i~~ll~~~P~il~~~~ 216 (392)
++.+.|.+++++.++++++++++|+++|++.++|..++.++|++++.+.
T Consensus 219 l~~~~~~~~~~~~l~~~~~~i~~~g~~p~~~~~v~~~~~~~~~~~~~i~~kv~~l~~~Gf~~~di~~~~~k~P~~l~~s~ 298 (413)
T KOG1267|consen 219 LESQPRPVLLYLKLKARLPFLLTLGFDPKTREFVKAPILLSYSSEKTLEPKVEVLKSLGFSREEIWKMVKKCPQILGYSV 298 (413)
T ss_pred HhcCccceeeehhhhhhhhhHHHhccCCchhHHHhhhhhhcccccccHHHHHHHHHHcCCCHHHHHHHHHhCchheEeeh
Confidence 2334455555578889999999999999999999999999999999999
Q ss_pred hhHHHHHHHHHHhCCCCCchhHHHHHHHHHhcCHHHHHHHHHHHHHcCCCHHHHHHHHHhCCccccccHH-HHHHHHHHH
Q 046450 217 ELFKNVVDVIKEMGFEPSSKSFILAVRSMAMSSKATWQRKKEILISFGWSEDEFRMVFKRQPLFMMASAK-KIRKLMDFF 295 (392)
Q Consensus 217 ~~~~~~v~~L~~lG~~~~~~~~~~~~~~~~~~s~~~l~~kv~fL~~lG~s~~ei~~~i~~~P~iL~~s~e-~L~~~~~fL 295 (392)
+++..+++++.+. .++ +...+.++..++..+.++++|+..+|++..++..|+.++|+++.+|++ .++++.+|+
T Consensus 299 ~~~~~~~~~~~~~--~~~----~~k~p~~l~~s~~~l~~~ie~l~~~g~~~~q~~~~~~~~Pq~l~~s~~~~~~~~~~~~ 372 (413)
T KOG1267|consen 299 KKNLKTTEYLLKN--PKH----ILKFPQLLRSSEDKLKPRIEFLLSLGFSDVQILEMVKRFPQYLSFSLEKILKRKYEYL 372 (413)
T ss_pred hhhhHHHHHHHhc--chh----hhhhhhhhhccchhhhhhHHHHHHcCCcHHHHHHHHhhccHHhhhhHHhhhhhhHHHH
Confidence 9888888888765 222 334444458899999999999999999999999999999999999999 899999999
Q ss_pred HHhhCCChhhHhcCCcccccCCCCccchhHHHHHHHHHc
Q 046450 296 VNKIGLEPSDIARYPNLLIGSLEKKVLPRWSVLQVLMSK 334 (392)
Q Consensus 296 ~~~~G~~~~~i~~~P~lL~~sle~~l~pR~~~l~~L~~~ 334 (392)
.+.|+++.++++.+|++++|++|.|+.||+.++..+..+
T Consensus 373 ~~~~~~p~~~~~~~p~~~~y~le~ri~pr~~~~~~~~~~ 411 (413)
T KOG1267|consen 373 LKGLLRPLSALVSFPAFFGYSLEKRIRPRFNVIKKLGVK 411 (413)
T ss_pred HHHcCchHHHHhccchhhccchhhcchhHHHHHHHHhcc
Confidence 999999999999999999999999999999987765543
No 6
>KOG1267 consensus Mitochondrial transcription termination factor, mTERF [Transcription; General function prediction only]
Probab=99.75 E-value=6.5e-18 Score=169.39 Aligned_cols=210 Identities=25% Similarity=0.389 Sum_probs=166.8
Q ss_pred chhHHHHHHHhCCCCchhHHHhhhcCccccccccccchhhHHHHHHhhccCCchHHHHHhhCcceeccCcccchhhhHHH
Q 046450 111 VLKPKIEYLESLGISGPDLAKILCPYPELLSRSLENHIIPTFDFLKGVFQANGNLVYALKQSIRVVNSDIQKRVVPNMNT 190 (392)
Q Consensus 111 ~l~p~v~fL~~lGls~~~l~~il~~~P~lL~~~~~~~l~p~v~fL~~lg~~~~~i~~il~~~P~lL~~s~~~~l~~~v~~ 190 (392)
+-...+++|++.|++..++.+++..+|.++..+.++.+.|+..+|+..|.+...+.+++...|.+|+.+.+.++.+.++|
T Consensus 90 ~p~s~~~~l~s~g~~~~~i~s~i~~~p~ll~~~~~~~l~~~~~~l~~~g~~~s~l~~i~s~~~~il~~~~~~~~~~~~~~ 169 (413)
T KOG1267|consen 90 NPSSVLSSLRSLGFTDSQISSIILSSPKLLYLSSENILKPKLRLLDSLGLPSSELSSIVSVVPKILLKSKGESLSTFIEF 169 (413)
T ss_pred CcHHHHHHHHhcCCchhhcccccccCchhhhccchhhhhhhhhhhhccCccccccchhhhccHHHHHhhcCCchhhHHHH
Confidence 35677899999999999999999999999999999999999999999999999999999888888876555456666665
Q ss_pred HHH-----------------------------------CCCCchhhhcccccCCceeeechhhHHHHHHHHHHhCCCCCc
Q 046450 191 LRA-----------------------------------HGVPEPHIARLIMLQPPSLVLRAELFKNVVDVIKEMGFEPSS 235 (392)
Q Consensus 191 L~~-----------------------------------lGv~~~~i~~ll~~~P~il~~~~~~~~~~v~~L~~lG~~~~~ 235 (392)
+++ +|..+.++..++...|+.+.... .+...+.++.++|+++.+
T Consensus 170 l~~~~~~~~~s~~~~~~~~~~~~~~~~~~v~~~~~~~~lg~~~~~L~~~l~~~~~~~~~~~-~l~~~~~~i~~~g~~p~~ 248 (413)
T KOG1267|consen 170 LKSIPPELLSSVVERLLTPVPSFLLNENSVERLDIRRELGVKPRLLKSLLESQPRPVLLYL-KLKARLPFLLTLGFDPKT 248 (413)
T ss_pred hhccchhhhhhHHHHhccccccccccccccccchhhHHhCCCHHHHHHHHhcCccceeeeh-hhhhhhhhHHHhccCCch
Confidence 555 44555556666666666554433 677788888999999999
Q ss_pred hhHHHHHHHHHhcCHHHHHHHHHHHHHcCCCHHHHHHHHHhCCccccccHHHHHHHHHHHHHhhCCChhhHhcCCccccc
Q 046450 236 KSFILAVRSMAMSSKATWQRKKEILISFGWSEDEFRMVFKRQPLFMMASAKKIRKLMDFFVNKIGLEPSDIARYPNLLIG 315 (392)
Q Consensus 236 ~~~~~~~~~~~~~s~~~l~~kv~fL~~lG~s~~ei~~~i~~~P~iL~~s~e~L~~~~~fL~~~~G~~~~~i~~~P~lL~~ 315 (392)
..++.++..+...+++++++|+++|+++||+.+||..|+.++|++|++|.+++..++.|+.+. .+++.++|+++.+
T Consensus 249 ~~~v~~~~~~~~~~~~~i~~kv~~l~~~Gf~~~di~~~~~k~P~~l~~s~~~~~~~~~~~~~~----~~~~~k~p~~l~~ 324 (413)
T KOG1267|consen 249 REFVKAPILLSYSSEKTLEPKVEVLKSLGFSREEIWKMVKKCPQILGYSVKKNLKTTEYLLKN----PKHILKFPQLLRS 324 (413)
T ss_pred hHHHhhhhhhcccccccHHHHHHHHHHcCCCHHHHHHHHHhCchheEeehhhhhHHHHHHHhc----chhhhhhhhhhhc
Confidence 889999999999999999999999999999999999999999999999999765555555553 2225555555544
Q ss_pred CCCCccchhHH
Q 046450 316 SLEKKVLPRWS 326 (392)
Q Consensus 316 sle~~l~pR~~ 326 (392)
+.. .+.+|++
T Consensus 325 s~~-~l~~~ie 334 (413)
T KOG1267|consen 325 SED-KLKPRIE 334 (413)
T ss_pred cch-hhhhhHH
Confidence 433 4555544
No 7
>smart00733 Mterf Mitochondrial termination factor repeats. Human mitochondrial termination factor is a DNA-binding protein that acts as a transcription termination factor. Six repeats occur in human mTERF, that also are present in numerous plant proteins.
Probab=97.18 E-value=0.00035 Score=42.46 Aligned_cols=30 Identities=23% Similarity=0.522 Sum_probs=26.5
Q ss_pred HHHHhCCccccccHHHHHHHHHHHHHhhCCC
Q 046450 272 MVFKRQPLFMMASAKKIRKLMDFFVNKIGLE 302 (392)
Q Consensus 272 ~~i~~~P~iL~~s~e~L~~~~~fL~~~~G~~ 302 (392)
+++.++|.++.++.++++++++||. ++|++
T Consensus 2 ~~~~~~P~il~~~~~~l~~~~~~l~-~~g~~ 31 (31)
T smart00733 2 KILKKFPQILGYSEKKLKPKVEFLK-ELGFS 31 (31)
T ss_pred chhhhCcCcccccHHHhhHHHHHHH-HcCCC
Confidence 4788999999999889999999999 58874
No 8
>smart00733 Mterf Mitochondrial termination factor repeats. Human mitochondrial termination factor is a DNA-binding protein that acts as a transcription termination factor. Six repeats occur in human mTERF, that also are present in numerous plant proteins.
Probab=96.85 E-value=0.00064 Score=41.23 Aligned_cols=28 Identities=21% Similarity=0.427 Sum_probs=12.9
Q ss_pred HHhhCcceeccCcccchhhhHHHHHHCCC
Q 046450 168 ALKQSIRVVNSDIQKRVVPNMNTLRAHGV 196 (392)
Q Consensus 168 il~~~P~lL~~s~~~~l~~~v~~L~~lGv 196 (392)
++.++|.+|+++ +++++++++||+++|+
T Consensus 3 ~~~~~P~il~~~-~~~l~~~~~~l~~~g~ 30 (31)
T smart00733 3 ILKKFPQILGYS-EKKLKPKVEFLKELGF 30 (31)
T ss_pred hhhhCcCccccc-HHHhhHHHHHHHHcCC
Confidence 344444444444 3334444444444443
No 9
>PF11955 PORR: Plant organelle RNA recognition domain; InterPro: IPR021099 The plant organelle RNA recognition (PORR) domain, previously known as DUF860, is a component of group II intron ribonucleoprotein particles in maize chloroplasts. It is required for the splicing of the introns with which it associates, and promotes splicing in the context of a heterodimer with the RNase III-domain protein RNC1. Proteins containing this domain are predicted to localise to mitochondria or chloroplasts []. It seems likely that most PORR proteins function in organellar RNA metabolism [].
Probab=92.53 E-value=0.73 Score=44.96 Aligned_cols=226 Identities=16% Similarity=0.178 Sum_probs=121.6
Q ss_pred hhhCCCChHHHHHHHHhCCceeccCc---C----CchhHHHHHHH--hCCCCchhHHHhhhcCccccccccccch-hhHH
Q 046450 83 LTSRGFTKPQIATLISKYPRILSHDP---E----KVLKPKIEYLE--SLGISGPDLAKILCPYPELLSRSLENHI-IPTF 152 (392)
Q Consensus 83 L~~lGl~~~~i~~ll~~~P~lL~~~~---~----~~l~p~v~fL~--~lGls~~~l~~il~~~P~lL~~~~~~~l-~p~v 152 (392)
-..+|+....+...+.+||.++.... . -.+.|...-|. +..+-.+.-..++.+--.+|-++.++.| ..++
T Consensus 44 ~~~L~l~~~~~~~flrkyP~iF~~~~~~~~~~~~~~LT~~a~~L~~eE~~~~~~~e~~~v~rL~KLLMMS~~~rlpL~ki 123 (335)
T PF11955_consen 44 RRQLGLKPRKVSRFLRKYPSIFEVFQHPSRSVPWFRLTPEAEDLLREERRVREEMEPDLVERLRKLLMMSKDRRLPLSKI 123 (335)
T ss_pred HHhcCCCcccHHHHHHhCCceEEEeccCCCCCceEEeCHHHHHHHHHHHHHHHhChHHHHHHHHHHhccCCCCcccHHHH
Confidence 34689976889999999999886532 1 12334443332 1222111223334444456666665433 2356
Q ss_pred HHHH-hhccCCchHHHHHhhCcceeccCc---ccchhhhHHHHHHCCCCchhhhccc-------------ccCCcee--e
Q 046450 153 DFLK-GVFQANGNLVYALKQSIRVVNSDI---QKRVVPNMNTLRAHGVPEPHIARLI-------------MLQPPSL--V 213 (392)
Q Consensus 153 ~fL~-~lg~~~~~i~~il~~~P~lL~~s~---~~~l~~~v~~L~~lGv~~~~i~~ll-------------~~~P~il--~ 213 (392)
..++ ++|++++-...++.+||..|.... ....-.-+.+=.++.++.-+..... ..+|--+ +
T Consensus 124 ~~l~~dLGLP~Df~~~lv~~yP~~Frvv~~~~~~~~LeLv~Wd~~LAvs~~E~~~~~~~~~~~~~~~~~~~~Fp~~fp~G 203 (335)
T PF11955_consen 124 AHLRRDLGLPDDFRDSLVPKYPDYFRVVDLEDGGRYLELVSWDPELAVSALEKRAEKEYREKREDGFDRPLAFPVSFPKG 203 (335)
T ss_pred HHHHHHcCCChhhccchhhhCCCCcEEeecCCCCCEEEEeecCCccCcCccchhhhhccccccccccCCceeeeecCCCC
Confidence 6665 699999988999999999887532 1111122222123444332221110 1122111 1
Q ss_pred ech-hhHHHHHHHHHHhCC----------CCCchhH-HHHHHH---HHhc--CHHHHHHHHHHHH-HcCCCHHHHHHHHH
Q 046450 214 LRA-ELFKNVVDVIKEMGF----------EPSSKSF-ILAVRS---MAMS--SKATWQRKKEILI-SFGWSEDEFRMVFK 275 (392)
Q Consensus 214 ~~~-~~~~~~v~~L~~lG~----------~~~~~~~-~~~~~~---~~~~--s~~~l~~kv~fL~-~lG~s~~ei~~~i~ 275 (392)
... .+..++++-++++-+ ++++..+ .++..+ ++.+ .......++..|+ .+|++ +.+..++.
T Consensus 204 ~~l~k~~~~~l~~fQ~lPy~SPYed~~~l~~~s~~~EKRaVaVlHElLSLTveKr~~~~~L~~fr~ef~lp-~k~~~~l~ 282 (335)
T PF11955_consen 204 FRLKKKFREWLEEFQKLPYISPYEDASHLDPGSDEAEKRAVAVLHELLSLTVEKRTEVDHLTHFRKEFGLP-QKFRRLLL 282 (335)
T ss_pred ccccHHHHHHHHHHhcCCCCCCCCCccCCCCCChHHHhHHHHHHHHHHHhhhhhhccHHHHHHHHHHhCCc-HHHHHHHH
Confidence 222 356677777766543 3333222 234333 2333 3334667788888 89998 57788999
Q ss_pred hCCccccccHHHHHHHHHHHHHhhCCChhh-HhcCCcc
Q 046450 276 RQPLFMMASAKKIRKLMDFFVNKIGLEPSD-IARYPNL 312 (392)
Q Consensus 276 ~~P~iL~~s~e~L~~~~~fL~~~~G~~~~~-i~~~P~l 312 (392)
+||.|+-.|... +.-.=||++ ++..++ |-++|.+
T Consensus 283 rHPgIFYvS~kg-~~~TVfLrE--AY~~~~Liek~Pl~ 317 (335)
T PF11955_consen 283 RHPGIFYVSLKG-KRHTVFLRE--AYDGGELIEKHPLV 317 (335)
T ss_pred hCCCeEEEeccC-CceEEEEee--ccCCCCCCCCCchH
Confidence 999999988761 111224444 444444 3466754
No 10
>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domain
Probab=90.25 E-value=0.45 Score=41.93 Aligned_cols=48 Identities=21% Similarity=0.378 Sum_probs=26.8
Q ss_pred HHHHHHHHHhCCCCCch-hHHHHHHHHHhcCHHHHHHHHHHHHHcCCCHHHHHHH
Q 046450 220 KNVVDVIKEMGFEPSSK-SFILAVRSMAMSSKATWQRKKEILISFGWSEDEFRMV 273 (392)
Q Consensus 220 ~~~v~~L~~lG~~~~~~-~~~~~~~~~~~~s~~~l~~kv~fL~~lG~s~~ei~~~ 273 (392)
...++.++.+|+++++. ..-..+.. ..=....+||.++|++.+++..+
T Consensus 119 ~~w~~l~~~~g~~~~~m~~wh~~fe~------~~p~~h~~~l~~~g~~~~~~~~i 167 (172)
T cd04790 119 EKWVAILKAAGMDEADMRRWHIEFEK------MEPEAHQEFLQSLGIPEDEIERI 167 (172)
T ss_pred HHHHHHHHHcCCChHHHHHHHHHHHH------hCcHHHHHHHHHcCCCHHHHHHH
Confidence 44555556677776541 11111110 01123567999999999998654
No 11
>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domain
Probab=74.13 E-value=6.2 Score=34.70 Aligned_cols=24 Identities=21% Similarity=0.243 Sum_probs=18.7
Q ss_pred hHHHhhhhCCCChHHHHHHHHhCC
Q 046450 78 SSIQLLTSRGFTKPQIATLISKYP 101 (392)
Q Consensus 78 ~~l~~L~~lGl~~~~i~~ll~~~P 101 (392)
..+..|+++|++-++|..++....
T Consensus 49 ~~I~~lr~~G~sL~eI~~ll~~~~ 72 (172)
T cd04790 49 EQICAYRSAGVSLEDIRSLLQQPG 72 (172)
T ss_pred HHHHHHHHcCCCHHHHHHHHhcCC
Confidence 457778899999999988887543
No 12
>PF04695 Pex14_N: Peroxisomal membrane anchor protein (Pex14p) conserved region; InterPro: IPR006785 This conserved region defines a group of peroxisomal membrane anchor proteins which bind the PTS1 (peroxisomal targeting signal) receptor and are required for the import of PTS1-containing proteins into peroxisomes. Loss of functional Pex14p results in defects in both the PTS1 and PTS2-dependent import pathways. Deletion analysis of this conserved region implicates it in selective peroxisome degradation. In the majority of members this region is situated at the N terminus of the protein [, ].; GO: 0005777 peroxisome, 0016020 membrane; PDB: 2W85_A 2W84_A 3FF5_B.
Probab=70.94 E-value=7.6 Score=32.72 Aligned_cols=31 Identities=23% Similarity=0.204 Sum_probs=23.2
Q ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHhCCccc
Q 046450 251 ATWQRKKEILISFGWSEDEFRMVFKRQPLFM 281 (392)
Q Consensus 251 ~~l~~kv~fL~~lG~s~~ei~~~i~~~P~iL 281 (392)
.-+.+|++||++=|++.+||..++.+.+.--
T Consensus 21 sp~~~k~~FL~sKGLt~~EI~~al~~a~~~~ 51 (136)
T PF04695_consen 21 SPLEKKIAFLESKGLTEEEIDEALGRAGSPP 51 (136)
T ss_dssp S-HHHHHHHHHHCT--HHHHHHHHHHHT--S
T ss_pred CCHHHHHHHHHcCCCCHHHHHHHHHhcCCcc
Confidence 3478999999999999999999999977655
No 13
>PF04695 Pex14_N: Peroxisomal membrane anchor protein (Pex14p) conserved region; InterPro: IPR006785 This conserved region defines a group of peroxisomal membrane anchor proteins which bind the PTS1 (peroxisomal targeting signal) receptor and are required for the import of PTS1-containing proteins into peroxisomes. Loss of functional Pex14p results in defects in both the PTS1 and PTS2-dependent import pathways. Deletion analysis of this conserved region implicates it in selective peroxisome degradation. In the majority of members this region is situated at the N terminus of the protein [, ].; GO: 0005777 peroxisome, 0016020 membrane; PDB: 2W85_A 2W84_A 3FF5_B.
Probab=70.20 E-value=5.6 Score=33.53 Aligned_cols=27 Identities=30% Similarity=0.462 Sum_probs=14.7
Q ss_pred hhHHHHHHHhCCCCchhHHHhhhcCcc
Q 046450 112 LKPKIEYLESLGISGPDLAKILCPYPE 138 (392)
Q Consensus 112 l~p~v~fL~~lGls~~~l~~il~~~P~ 138 (392)
+..|++||++.|++.++|..++.+.+.
T Consensus 23 ~~~k~~FL~sKGLt~~EI~~al~~a~~ 49 (136)
T PF04695_consen 23 LEKKIAFLESKGLTEEEIDEALGRAGS 49 (136)
T ss_dssp HHHHHHHHHHCT--HHHHHHHHHHHT-
T ss_pred HHHHHHHHHcCCCCHHHHHHHHHhcCC
Confidence 455666666666666666666655443
No 14
>PF11955 PORR: Plant organelle RNA recognition domain; InterPro: IPR021099 The plant organelle RNA recognition (PORR) domain, previously known as DUF860, is a component of group II intron ribonucleoprotein particles in maize chloroplasts. It is required for the splicing of the introns with which it associates, and promotes splicing in the context of a heterodimer with the RNase III-domain protein RNC1. Proteins containing this domain are predicted to localise to mitochondria or chloroplasts []. It seems likely that most PORR proteins function in organellar RNA metabolism [].
Probab=66.85 E-value=27 Score=34.15 Aligned_cols=33 Identities=15% Similarity=0.111 Sum_probs=28.4
Q ss_pred HHHHHHHHH-HcCCCHHHHHHHHHhCCccccccH
Q 046450 253 WQRKKEILI-SFGWSEDEFRMVFKRQPLFMMASA 285 (392)
Q Consensus 253 l~~kv~fL~-~lG~s~~ei~~~i~~~P~iL~~s~ 285 (392)
--.++..++ .+|++.+-...++.++|+.+..-.
T Consensus 119 pL~ki~~l~~dLGLP~Df~~~lv~~yP~~Frvv~ 152 (335)
T PF11955_consen 119 PLSKIAHLRRDLGLPDDFRDSLVPKYPDYFRVVD 152 (335)
T ss_pred cHHHHHHHHHHcCCChhhccchhhhCCCCcEEee
Confidence 356788888 999999999999999999988744
No 15
>COG1125 OpuBA ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]
Probab=59.54 E-value=21 Score=33.67 Aligned_cols=66 Identities=24% Similarity=0.387 Sum_probs=48.2
Q ss_pred CHHHHHHHHHHHH-HcCC-CHHHHHHHHHhCCccccccHHHHHHHHHHHHHhhCCChhhH-hcCCcccc
Q 046450 249 SKATWQRKKEILI-SFGW-SEDEFRMVFKRQPLFMMASAKKIRKLMDFFVNKIGLEPSDI-ARYPNLLI 314 (392)
Q Consensus 249 s~~~l~~kv~fL~-~lG~-s~~ei~~~i~~~P~iL~~s~e~L~~~~~fL~~~~G~~~~~i-~~~P~lL~ 314 (392)
..-.+++++.|.- ..|+ +.-.|.+=|...|.+++++.++++.+.+-|.+-+|+++++. -+||.=|+
T Consensus 69 d~~~LRr~IGYviQqigLFPh~Tv~eNIa~VP~L~~w~k~~i~~r~~ELl~lvgL~p~~~~~RyP~eLS 137 (309)
T COG1125 69 DPVELRRKIGYVIQQIGLFPHLTVAENIATVPKLLGWDKERIKKRADELLDLVGLDPSEYADRYPHELS 137 (309)
T ss_pred CHHHHHHhhhhhhhhcccCCCccHHHHHHhhhhhcCCCHHHHHHHHHHHHHHhCCCHHHHhhcCchhcC
Confidence 3456777888776 5554 44456666778999999999999999999999899987543 35555443
No 16
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=58.04 E-value=16 Score=23.00 Aligned_cols=23 Identities=22% Similarity=0.427 Sum_probs=16.5
Q ss_pred HHHHHHHHcCCCHHHHHHHHHhC
Q 046450 255 RKKEILISFGWSEDEFRMVFKRQ 277 (392)
Q Consensus 255 ~kv~fL~~lG~s~~ei~~~i~~~ 277 (392)
.+++-|..+||+.+++.+.+..+
T Consensus 4 ~~v~~L~~mGf~~~~~~~AL~~~ 26 (37)
T PF00627_consen 4 EKVQQLMEMGFSREQAREALRAC 26 (37)
T ss_dssp HHHHHHHHHTS-HHHHHHHHHHT
T ss_pred HHHHHHHHcCCCHHHHHHHHHHc
Confidence 46677788888888887777664
No 17
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=55.65 E-value=20 Score=22.35 Aligned_cols=23 Identities=22% Similarity=0.408 Sum_probs=17.0
Q ss_pred HHHHHHHHcCCCHHHHHHHHHhC
Q 046450 255 RKKEILISFGWSEDEFRMVFKRQ 277 (392)
Q Consensus 255 ~kv~fL~~lG~s~~ei~~~i~~~ 277 (392)
.+++-|..+||+.+++...+.++
T Consensus 3 ~~v~~L~~mGf~~~~a~~aL~~~ 25 (37)
T smart00165 3 EKIDQLLEMGFSREEALKALRAA 25 (37)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHh
Confidence 45677778888888887776664
No 18
>PF11181 YflT: Heat induced stress protein YflT
Probab=55.59 E-value=46 Score=26.34 Aligned_cols=79 Identities=22% Similarity=0.292 Sum_probs=41.0
Q ss_pred ccchhhhHHHHHHCCCCchhhhcccccCCceeeechhhHHHHHHHH--HHhCCCCCchhHHHHHHHHHhcCHHHHHHHHH
Q 046450 181 QKRVVPNMNTLRAHGVPEPHIARLIMLQPPSLVLRAELFKNVVDVI--KEMGFEPSSKSFILAVRSMAMSSKATWQRKKE 258 (392)
Q Consensus 181 ~~~l~~~v~~L~~lGv~~~~i~~ll~~~P~il~~~~~~~~~~v~~L--~~lG~~~~~~~~~~~~~~~~~~s~~~l~~kv~ 258 (392)
+..+...|+-|+.-|+..++| .+++.+.++....-+.- ...|.++ ..|.-.+..++....+.++.
T Consensus 9 ~~E~~~~I~~L~~~Gy~~ddI--------~Vva~d~~~~~~l~~~t~~~~~~~~~--~~~~d~~~~~f~~~~d~~~~--- 75 (103)
T PF11181_consen 9 EEEALSAIEELKAQGYSEDDI--------YVVAKDKDRTERLADQTDTNTVGASE--ESFWDKIKNFFTSGGDELRS--- 75 (103)
T ss_pred HHHHHHHHHHHHHcCCCcccE--------EEEEcCchHHHHHHHhcCCceecccc--ccHHHHHHHhccCCcHHHHH---
Confidence 334778888899999999987 23333322222111111 1122222 22333333334334444443
Q ss_pred HHHHcCCCHHHHHH
Q 046450 259 ILISFGWSEDEFRM 272 (392)
Q Consensus 259 fL~~lG~s~~ei~~ 272 (392)
-|.++|++.+++.+
T Consensus 76 ~l~~lGl~~~ea~~ 89 (103)
T PF11181_consen 76 KLESLGLSEDEAER 89 (103)
T ss_pred HHHHcCCCHHHHHH
Confidence 45688999888764
No 19
>PRK14136 recX recombination regulator RecX; Provisional
Probab=52.79 E-value=2.1e+02 Score=27.61 Aligned_cols=106 Identities=17% Similarity=0.230 Sum_probs=58.5
Q ss_pred chhhHHHHHHhhcc-CCchHHHHHhhCcceeccCcccchhhhHHHHHHCCCCchhhhcccccCCceeeechhhHHHHHHH
Q 046450 147 HIIPTFDFLKGVFQ-ANGNLVYALKQSIRVVNSDIQKRVVPNMNTLRAHGVPEPHIARLIMLQPPSLVLRAELFKNVVDV 225 (392)
Q Consensus 147 ~l~p~v~fL~~lg~-~~~~i~~il~~~P~lL~~s~~~~l~~~v~~L~~lGv~~~~i~~ll~~~P~il~~~~~~~~~~v~~ 225 (392)
.+...|++|++.|+ ++......+.+. ..=... -...-.-|++-||+.+.|...+... ..+.+....+.
T Consensus 195 ~IE~VIerLke~gYLDDeRFAesyVr~-R~~kkG----p~rIrqELrQKGId~eLIEqALeei------eEDE~E~A~~L 263 (309)
T PRK14136 195 SVEPLLDALEREGWLSDARFAESLVHR-RASRVG----SARIVSELKRHAVGDALVESVGAQL------RETEFERAQAV 263 (309)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHHHHHH-Hhhchh----HHHHHHHHHHcCCCHHHHHHHHHhc------cHhHHHHHHHH
Confidence 46667778888776 445555554432 111111 2233466778999998887766522 11222222222
Q ss_pred HH-HhCCCCCchhHHHHHHHHHhcCHHHHHHHHHHHHHcCCCHHHHHHHHHhC
Q 046450 226 IK-EMGFEPSSKSFILAVRSMAMSSKATWQRKKEILISFGWSEDEFRMVFKRQ 277 (392)
Q Consensus 226 L~-~lG~~~~~~~~~~~~~~~~~~s~~~l~~kv~fL~~lG~s~~ei~~~i~~~ 277 (392)
++ .++-.+. ......+.+.||..-||+.+.|..++..+
T Consensus 264 ~eKK~~~~~~--------------d~kek~K~iRfL~rRGFS~D~I~~vLk~~ 302 (309)
T PRK14136 264 WRKKFGALPQ--------------TPAERAKQARFLAARGFSSATIVKLLKVG 302 (309)
T ss_pred HHHHhcccCc--------------CHHHHHHHHHHHHHCCCCHHHHHHHHHhc
Confidence 21 1221111 12234455789999999999998888654
No 20
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=52.45 E-value=24 Score=22.11 Aligned_cols=23 Identities=30% Similarity=0.524 Sum_probs=16.7
Q ss_pred HHHHHHHHcCCCHHHHHHHHHhC
Q 046450 255 RKKEILISFGWSEDEFRMVFKRQ 277 (392)
Q Consensus 255 ~kv~fL~~lG~s~~ei~~~i~~~ 277 (392)
.+++-|.++||+.+++...+..+
T Consensus 3 ~~v~~L~~mGf~~~~~~~AL~~~ 25 (38)
T cd00194 3 EKLEQLLEMGFSREEARKALRAT 25 (38)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHh
Confidence 45677778888888877766653
No 21
>PRK11613 folP dihydropteroate synthase; Provisional
Probab=47.62 E-value=71 Score=30.45 Aligned_cols=70 Identities=10% Similarity=0.089 Sum_probs=47.1
Q ss_pred HHHHHHHHHHHhhCCChhhHhcCCcccccCCCCccchhHHHHHHHHHcCCCCCCcccccccccChHHHHHHHhccCCC
Q 046450 287 KIRKLMDFFVNKIGLEPSDIARYPNLLIGSLEKKVLPRWSVLQVLMSKNLLKKDVNVSLALFVTKEVFERRFVTSYMH 364 (392)
Q Consensus 287 ~L~~~~~fL~~~~G~~~~~i~~~P~lL~~sle~~l~pR~~~l~~L~~~G~~~~~~~l~~~l~~s~~~F~~~~v~~~~e 364 (392)
-++.+++.+.+ .|++.+.|+--|- +++. ++...-+.+++.+.... ...++.++..|.++|...+.+.-++
T Consensus 164 ~l~~~i~~a~~-~GI~~~~IilDPG-iGF~--k~~~~n~~ll~~l~~l~----~lg~Pilvg~SRKsfig~~~~~~~~ 233 (282)
T PRK11613 164 YFIEQIARCEA-AGIAKEKLLLDPG-FGFG--KNLSHNYQLLARLAEFH----HFNLPLLVGMSRKSMIGQLLNVGPS 233 (282)
T ss_pred HHHHHHHHHHH-cCCChhhEEEeCC-CCcC--CCHHHHHHHHHHHHHHH----hCCCCEEEEecccHHHHhhcCCChh
Confidence 35667787777 7999999877785 4543 44556666655554421 2345678999999999888765443
No 22
>KOG0011 consensus Nucleotide excision repair factor NEF2, RAD23 component [Replication, recombination and repair]
Probab=47.45 E-value=12 Score=36.13 Aligned_cols=105 Identities=17% Similarity=0.241 Sum_probs=57.0
Q ss_pred hcCCCHHHHHhhcccccccCCCChhhHHHhhhhCCCChHHHHHHHHhCCceecc-----Cc---------CCchhHHHHH
Q 046450 53 SCGLSLEKAISVSKLVKIQDTEKPNSSIQLLTSRGFTKPQIATLISKYPRILSH-----DP---------EKVLKPKIEY 118 (392)
Q Consensus 53 ~~Gls~~~~~~i~~~~~~~~~~~~~~~l~~L~~lGl~~~~i~~ll~~~P~lL~~-----~~---------~~~l~p~v~f 118 (392)
++|..++++.++.+. .-++++..++||.. |+....-.......|..... .+ +..-..-++|
T Consensus 144 ~MGy~re~V~~AlRA----afNNPeRAVEYLl~-GIP~~~~~~~~~~~~~~~~~~p~~~~p~~~~~~~~~~~~~~~~l~f 218 (340)
T KOG0011|consen 144 EMGYDREEVERALRA----AFNNPERAVEYLLN-GIPEDAEVPEPEKSTAAAAELPANAQPLDLFPQGAVEASGGDPLEF 218 (340)
T ss_pred HhCccHHHHHHHHHH----hhCChhhhHHHHhc-CCcccccCCcccCCcccCCCCCCCCChhhcCCccchhhhcCCchhh
Confidence 467777777666543 22577778888875 55532110011111111111 11 1111233667
Q ss_pred HHhCCCCchhHHHhhhcCccccccccccchhhHHHHHHhhccCCchHHHHHhhCcc
Q 046450 119 LESLGISGPDLAKILCPYPELLSRSLENHIIPTFDFLKGVFQANGNLVYALKQSIR 174 (392)
Q Consensus 119 L~~lGls~~~l~~il~~~P~lL~~~~~~~l~p~v~fL~~lg~~~~~i~~il~~~P~ 174 (392)
|++. -.-..+..+|..+|.+|.. .|+.+|-..-++.+.|..++.
T Consensus 219 Lr~~-~qf~~lR~~iqqNP~ll~~-----------~Lqqlg~~nP~L~q~Iq~nqe 262 (340)
T KOG0011|consen 219 LRNQ-PQFQQLRQMIQQNPELLHP-----------LLQQLGKQNPQLLQLIQENQE 262 (340)
T ss_pred hhcc-HHHHHHHHHHhhCHHHHHH-----------HHHHHhhhCHHHHHHHHHHHH
Confidence 6643 1223577778888887652 567788888788888877665
No 23
>PF02022 Integrase_Zn: Integrase Zinc binding domain The structure of the N-terminal zinc binding domain.; InterPro: IPR003308 Retroviral integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains: an N-terminal zinc binding domain, a central catalytic core and a C-terminal DNA-binding domain [, ]. Often found as part of the POL polyprotein.; GO: 0008270 zinc ion binding; PDB: 1E0E_A 3F9K_F 1E27_C 1K6Y_B 1WJD_A 1WJB_A 1WJF_A 1WJE_B 3HPG_B 3HPH_C ....
Probab=45.59 E-value=41 Score=21.95 Aligned_cols=29 Identities=14% Similarity=0.250 Sum_probs=21.8
Q ss_pred HHHHHHHHHH-HcCCCHHHHHHHHHhCCcc
Q 046450 252 TWQRKKEILI-SFGWSEDEFRMVFKRQPLF 280 (392)
Q Consensus 252 ~l~~kv~fL~-~lG~s~~ei~~~i~~~P~i 280 (392)
++-.....|. ++|++..+..+||..+|..
T Consensus 7 k~H~n~~~L~~~f~ip~~vAk~IV~~C~~C 36 (40)
T PF02022_consen 7 KYHSNAKALRHKFGIPRLVAKQIVNQCPKC 36 (40)
T ss_dssp HHHH-HHHHHHHHT--HHHHHHHHHHSCCH
T ss_pred HHccCHHHHHHHHccCHHHHHHHHHHCHHH
Confidence 4455677888 8999999999999999975
No 24
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=45.49 E-value=62 Score=25.11 Aligned_cols=36 Identities=19% Similarity=0.252 Sum_probs=12.9
Q ss_pred HHHHhCCceeccCcCCchhHHHHHHH-hCCCCchhHH
Q 046450 95 TLISKYPRILSHDPEKVLKPKIEYLE-SLGISGPDLA 130 (392)
Q Consensus 95 ~ll~~~P~lL~~~~~~~l~p~v~fL~-~lGls~~~l~ 130 (392)
.+|..+|-.|..++..-=-.+++-+- ++|++.++-.
T Consensus 38 ~~l~~nPY~L~~~i~gi~F~~aD~iA~~~g~~~~d~~ 74 (94)
T PF14490_consen 38 EILKENPYRLIEDIDGIGFKTADKIALKLGIEPDDPR 74 (94)
T ss_dssp HHHHH-STCCCB-SSSSBHHHHHHHHHTTT--TT-HH
T ss_pred HHHHHChHHHHHHccCCCHHHHHHHHHHcCCCCCCHH
Confidence 44455555555543322223333333 4555544433
No 25
>PF07499 RuvA_C: RuvA, C-terminal domain; InterPro: IPR011114 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. The domain represents the C-terminal domain III of RuvA. This domain plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB []. Within the Holliday junction, this domain makes no interaction with the DNA.; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination, 0009379 Holliday junction helicase complex; PDB: 1HJP_A 1CUK_A 1C7Y_A 1IXS_A 1IXR_B 1BVS_E 2ZTC_A 2ZTD_B 2H5X_A.
Probab=45.07 E-value=43 Score=22.45 Aligned_cols=25 Identities=28% Similarity=0.399 Sum_probs=18.4
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHhC
Q 046450 253 WQRKKEILISFGWSEDEFRMVFKRQ 277 (392)
Q Consensus 253 l~~kv~fL~~lG~s~~ei~~~i~~~ 277 (392)
+..-++-|..+||+..++.+++.+-
T Consensus 3 ~~d~~~AL~~LGy~~~e~~~av~~~ 27 (47)
T PF07499_consen 3 LEDALEALISLGYSKAEAQKAVSKL 27 (47)
T ss_dssp HHHHHHHHHHTTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHh
Confidence 3455667788999999998888774
No 26
>TIGR01448 recD_rel helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.
Probab=44.73 E-value=47 Score=36.10 Aligned_cols=93 Identities=17% Similarity=0.206 Sum_probs=58.9
Q ss_pred hHHHhHh--hcCCCHHHHHhhcccccccCCCChhhHHHhhhhC-CCChHHHHHHHHhCCceeccCcCCchhHHHHHHHhC
Q 046450 46 TVSFLTH--SCGLSLEKAISVSKLVKIQDTEKPNSSIQLLTSR-GFTKPQIATLISKYPRILSHDPEKVLKPKIEYLESL 122 (392)
Q Consensus 46 ~v~~L~~--~~Gls~~~~~~i~~~~~~~~~~~~~~~l~~L~~l-Gl~~~~i~~ll~~~P~lL~~~~~~~l~p~v~fL~~l 122 (392)
.+.||.+ --|+-+..+.+|+..+.-+..+.++.-.+-|.++ |+++.....+...+... ......+.||.++
T Consensus 80 i~~yL~s~~~~GIG~~~A~~iv~~fg~~~~~~i~~~~~~L~~v~gi~~~~~~~i~~~~~~~------~~~~~~~~~L~~~ 153 (720)
T TIGR01448 80 IVAYLSSRSIKGVGKKLAQRIVKTFGEAAFDVLDDDPEKLLEVPGISKANLEKFVSQWSQQ------GDERRLLAGLQGL 153 (720)
T ss_pred HHHHHhcCCCCCcCHHHHHHHHHHhCHhHHHHHHhCHHHHhcCCCCCHHHHHHHHHHHHHh------HHHHHHHHHHHHc
Confidence 4588853 2467788899988776322222222223344443 88888888888876221 1256777899999
Q ss_pred CCCchhHHH-----------hhhcCcccccccc
Q 046450 123 GISGPDLAK-----------ILCPYPELLSRSL 144 (392)
Q Consensus 123 Gls~~~l~~-----------il~~~P~lL~~~~ 144 (392)
|++.....+ +|..+|+.|..++
T Consensus 154 gi~~~~a~ki~~~yg~~~~~~i~~nPY~L~~~i 186 (720)
T TIGR01448 154 GIGIKLAQRIYKFYQADTLDRVEKDPYLLAEDV 186 (720)
T ss_pred CCCHHHHHHHHHHHhHHHHHHHHhCchhhhhhc
Confidence 998765444 4677888776543
No 27
>PF11212 DUF2999: Protein of unknown function (DUF2999); InterPro: IPR021376 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=44.60 E-value=43 Score=24.78 Aligned_cols=56 Identities=25% Similarity=0.491 Sum_probs=36.6
Q ss_pred hhHHHhhhhCCCChHHHHHHHHhCCceeccCcCCchhHHHHHHHhCCCCchhHHHh---hhcCcccc
Q 046450 77 NSSIQLLTSRGFTKPQIATLISKYPRILSHDPEKVLKPKIEYLESLGISGPDLAKI---LCPYPELL 140 (392)
Q Consensus 77 ~~~l~~L~~lGl~~~~i~~ll~~~P~lL~~~~~~~l~p~v~fL~~lGls~~~l~~i---l~~~P~lL 140 (392)
++.++.|++..+|++++..++.. |+.+| .-....+..+|++++.+..+ +-.+|.++
T Consensus 2 NPIia~LKehnvsd~qi~elFq~----lT~NP----l~AMa~i~qLGip~eKLQ~lm~~VMqnP~Li 60 (82)
T PF11212_consen 2 NPIIAILKEHNVSDEQINELFQA----LTQNP----LAAMATIQQLGIPQEKLQQLMAQVMQNPALI 60 (82)
T ss_pred chHHHHHHHcCCCHHHHHHHHHH----HhhCH----HHHHHHHHHcCCCHHHHHHHHHHHhcChHHH
Confidence 46778888888888888877764 44433 22356677888888776544 44556553
No 28
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=41.57 E-value=44 Score=22.44 Aligned_cols=41 Identities=22% Similarity=0.530 Sum_probs=26.5
Q ss_pred HHHCCCCchhhhcccccCCceeeechhhHHHHHHHHHHhCCCCC
Q 046450 191 LRAHGVPEPHIARLIMLQPPSLVLRAELFKNVVDVIKEMGFEPS 234 (392)
Q Consensus 191 L~~lGv~~~~i~~ll~~~P~il~~~~~~~~~~v~~L~~lG~~~~ 234 (392)
-+.+|++..-+.+.+...|. .+.+.-+...+..+++|+.++
T Consensus 6 A~~agvS~~TVSr~ln~~~~---vs~~tr~rI~~~a~~lgY~pN 46 (46)
T PF00356_consen 6 AREAGVSKSTVSRVLNGPPR---VSEETRERILEAAEELGYRPN 46 (46)
T ss_dssp HHHHTSSHHHHHHHHTTCSS---STHHHHHHHHHHHHHHTB-SS
T ss_pred HHHHCcCHHHHHHHHhCCCC---CCHHHHHHHHHHHHHHCCCCC
Confidence 34578888888887776653 245555566666677777653
No 29
>PF03960 ArsC: ArsC family; InterPro: IPR006660 Several bacterial taxon have a chromosomal resistance system, encoded by the ars operon, for the detoxification of arsenate, arsenite, and antimonite []. This system transports arsenite and antimonite out of the cell. The pump is composed of two polypeptides, the products of the arsA and arsB genes. This two-subunit enzyme produces resistance to arsenite and antimonite. Arsenate, however, must first be reduced to arsenite before it is extruded. A third gene, arsC, expands the substrate specificity to allow for arsenate pumping and resistance. ArsC is an approximately 150-residue arsenate reductase that uses reduced glutathione (GSH) to convert arsenate to arsenite with a redox active cysteine residue in the active site. ArsC forms an active quaternary complex with GSH, arsenate, and glutaredoxin 1 (Grx1). The three ligands must be present simultaneously for reduction to occur []. The arsC family also comprises the Spx proteins which are GRAM-positive bacterial transcription factors that regulate the transcription of multiple genes in response to disulphide stress []. The arsC protein structure has been solved []. It belongs to the thioredoxin superfamily fold which is defined by a beta-sheet core surrounded by alpha-helices. The active cysteine residue of ArsC is located in the loop between the first beta-strand and the first helix, which is also conserved in the Spx protein and its homologues.; PDB: 2KOK_A 1SK1_A 1SK2_A 1JZW_A 1J9B_A 1S3C_A 1SD8_A 1SD9_A 1I9D_A 1SK0_A ....
Probab=36.75 E-value=40 Score=26.93 Aligned_cols=20 Identities=30% Similarity=0.599 Sum_probs=8.9
Q ss_pred CCchhHHHhhhcCccccccc
Q 046450 124 ISGPDLAKILCPYPELLSRS 143 (392)
Q Consensus 124 ls~~~l~~il~~~P~lL~~~ 143 (392)
++.+++..++..+|.++.++
T Consensus 71 ~s~~e~i~~l~~~p~LikRP 90 (110)
T PF03960_consen 71 LSDEELIELLLENPKLIKRP 90 (110)
T ss_dssp SBHHHHHHHHHHSGGGB-SS
T ss_pred hhhHHHHHHHHhChhheeCC
Confidence 44444444444444444444
No 30
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=33.33 E-value=67 Score=19.58 Aligned_cols=24 Identities=21% Similarity=0.292 Sum_probs=14.4
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHh
Q 046450 253 WQRKKEILISFGWSEDEFRMVFKR 276 (392)
Q Consensus 253 l~~kv~fL~~lG~s~~ei~~~i~~ 276 (392)
|..-+.--+..|+|.+|+...+..
T Consensus 5 W~~Li~eA~~~Gls~eeir~FL~~ 28 (30)
T PF08671_consen 5 WVELIKEAKESGLSKEEIREFLEF 28 (30)
T ss_dssp HHHHHHHHHHTT--HHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHh
Confidence 444444555789999998877654
No 31
>PRK08561 rps15p 30S ribosomal protein S15P; Reviewed
Probab=33.14 E-value=93 Score=26.67 Aligned_cols=114 Identities=13% Similarity=0.151 Sum_probs=54.8
Q ss_pred ccCCceeeechhhHHHHHHHHHHhCCCCCchhHHHH----HHHHHhcCHHHHHHHHHHHHHcCCCHHHHHHHHHhCCccc
Q 046450 206 MLQPPSLVLRAELFKNVVDVIKEMGFEPSSKSFILA----VRSMAMSSKATWQRKKEILISFGWSEDEFRMVFKRQPLFM 281 (392)
Q Consensus 206 ~~~P~il~~~~~~~~~~v~~L~~lG~~~~~~~~~~~----~~~~~~~s~~~l~~kv~fL~~lG~s~~ei~~~i~~~P~iL 281 (392)
...|..+..+.+.+++.+--|..-|+++.++..+.. .+.+-. .+..-|.+++..+-.--
T Consensus 20 ~~~P~W~~~~~eeve~~I~~lakkG~~pSqIG~~LRD~~gip~Vk~-----------------vtG~ki~~iLk~~gl~p 82 (151)
T PRK08561 20 TEPPEWVDYSPEEIEELVVELAKQGYSPSMIGIILRDQYGIPDVKL-----------------ITGKKITEILEENGLAP 82 (151)
T ss_pred CCCCccccCCHHHHHHHHHHHHHCCCCHHHhhhhHhhccCCCceee-----------------eccchHHHHHHHcCCCC
Confidence 345666666777777777777777776665433210 000000 00112222222222222
Q ss_pred cccHH--HHHHHHHHHHHhhCCChhhHhcCCcccccCCCCccchhHHHHHHHHHcCCCCCCc
Q 046450 282 MASAK--KIRKLMDFFVNKIGLEPSDIARYPNLLIGSLEKKVLPRWSVLQVLMSKNLLKKDV 341 (392)
Q Consensus 282 ~~s~e--~L~~~~~fL~~~~G~~~~~i~~~P~lL~~sle~~l~pR~~~l~~L~~~G~~~~~~ 341 (392)
.+..| .|..++..|.+++.....|...-=.++ ...-.|.+.+++++..+.++.++
T Consensus 83 ~iPEDL~~L~~ri~~L~~HL~~nkKD~~skRgL~-----~~~skrrRLl~Yyk~~~~LP~~W 139 (151)
T PRK08561 83 EIPEDLRNLIKKAVNLRKHLEENPKDLHNKRGLQ-----LIESKIRRLVKYYKRTGVLPADW 139 (151)
T ss_pred CCcHHHHHHHHHHHHHHHHHHhCCCcchhHHHHH-----HHHHHHHHHHHHHHhcCCCCCCC
Confidence 22333 455667777776666655542111111 11224556677888877765443
No 32
>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription]
Probab=33.06 E-value=67 Score=27.99 Aligned_cols=20 Identities=10% Similarity=0.217 Sum_probs=10.9
Q ss_pred CCCHHHHHHHHHhCCccccc
Q 046450 264 GWSEDEFRMVFKRQPLFMMA 283 (392)
Q Consensus 264 G~s~~ei~~~i~~~P~iL~~ 283 (392)
+-+.+.|.+++..||.++-.
T Consensus 146 ~~~l~vI~~LL~~~~AVlV~ 165 (187)
T COG3620 146 DESLNVISQLLEEHPAVLVV 165 (187)
T ss_pred CCCHHHHHHHHhhCCeEEEE
Confidence 44455555555566655544
No 33
>PF02787 CPSase_L_D3: Carbamoyl-phosphate synthetase large chain, oligomerisation domain; InterPro: IPR005480 Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates [, ]. CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate []. The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC). Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain []. CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites []. The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain. Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein []. The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP []. There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia []. CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains []. This entry represents the oligomerisation domain found in the large subunit of carbamoyl phosphate synthases as well as in certain other carboxy phsophate domain-containing enzymes.; GO: 0006807 nitrogen compound metabolic process; PDB: 1M6V_C 1CS0_C 1C30_E 1C3O_G 1BXR_A 1T36_E 1A9X_A 1KEE_G 1CE8_A 1JDB_H ....
Probab=32.21 E-value=83 Score=25.97 Aligned_cols=70 Identities=21% Similarity=0.250 Sum_probs=31.7
Q ss_pred hhhhHHHHHHCCCCchhhhcccccCCceeeechhhHHHHHHHHHHhCCCCCchhHHHHHHHHHhcCHHHHHHHHHHHHHc
Q 046450 184 VVPNMNTLRAHGVPEPHIARLIMLQPPSLVLRAELFKNVVDVIKEMGFEPSSKSFILAVRSMAMSSKATWQRKKEILISF 263 (392)
Q Consensus 184 l~~~v~~L~~lGv~~~~i~~ll~~~P~il~~~~~~~~~~v~~L~~lG~~~~~~~~~~~~~~~~~~s~~~l~~kv~fL~~l 263 (392)
+-...+.| +.|++.++|..+=.-+|+.| .++++.++.=+++ .....+.-...+.-.+++
T Consensus 13 lf~i~eAl-rrG~sveeI~e~T~ID~wFL----~~i~~Iv~~e~~L----------------~~~~~~~~~~~L~~aK~~ 71 (123)
T PF02787_consen 13 LFAIAEAL-RRGYSVEEIHELTKIDPWFL----EQIKNIVDMEKEL----------------KEYLNELDPELLRKAKRL 71 (123)
T ss_dssp HHHHHHHH-HTTB-HHHHHHHH---HHHH----HHHHHHHHHHHHH----------------HHHGGG--HHHHHHHHHT
T ss_pred HHHHHHHH-HcCCCHHHHHHHHCccHHHH----HHHHHHHHHHHHH----------------HHhhccchHHHHHHHHHc
Confidence 44444444 35888888887766677765 2233333221111 000001112233445689
Q ss_pred CCCHHHHHHHH
Q 046450 264 GWSEDEFRMVF 274 (392)
Q Consensus 264 G~s~~ei~~~i 274 (392)
|||..+|+++.
T Consensus 72 GFsD~~IA~l~ 82 (123)
T PF02787_consen 72 GFSDRQIARLW 82 (123)
T ss_dssp T--HHHHHHHH
T ss_pred CCCHHHHHhcc
Confidence 99999998774
No 34
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=32.10 E-value=58 Score=29.04 Aligned_cols=25 Identities=8% Similarity=-0.079 Sum_probs=16.4
Q ss_pred hhhHHHHHHhhccCCchHHHHHhhC
Q 046450 148 IIPTFDFLKGVFQANGNLVYALKQS 172 (392)
Q Consensus 148 l~p~v~fL~~lg~~~~~i~~il~~~ 172 (392)
+...+.+|.++|++..++.+++.++
T Consensus 149 ~~ev~~aL~~LG~~~~~a~~~~~~~ 173 (192)
T PRK00116 149 LEEAVSALVALGYKPKEASKAVAKI 173 (192)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 4556667777777776666666654
No 35
>TIGR01448 recD_rel helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.
Probab=31.96 E-value=1.1e+02 Score=33.29 Aligned_cols=99 Identities=16% Similarity=0.228 Sum_probs=66.4
Q ss_pred CCCChhhHHHhhhh---CCCChHHHHHHHHhCCceeccCcCCchhHHHHHHHhC-CCCchhHHHhhhcCccccccccccc
Q 046450 72 DTEKPNSSIQLLTS---RGFTKPQIATLISKYPRILSHDPEKVLKPKIEYLESL-GISGPDLAKILCPYPELLSRSLENH 147 (392)
Q Consensus 72 ~~~~~~~~l~~L~~---lGl~~~~i~~ll~~~P~lL~~~~~~~l~p~v~fL~~l-Gls~~~l~~il~~~P~lL~~~~~~~ 147 (392)
.+.+.+..+.||.+ .|+.+....+++..++. +.-+.+....+-|.++ |++.+.+..+...+... ..
T Consensus 73 ~p~~~~~i~~yL~s~~~~GIG~~~A~~iv~~fg~----~~~~~i~~~~~~L~~v~gi~~~~~~~i~~~~~~~------~~ 142 (720)
T TIGR01448 73 APTSKEGIVAYLSSRSIKGVGKKLAQRIVKTFGE----AAFDVLDDDPEKLLEVPGISKANLEKFVSQWSQQ------GD 142 (720)
T ss_pred CCCCHHHHHHHHhcCCCCCcCHHHHHHHHHHhCH----hHHHHHHhCHHHHhcCCCCCHHHHHHHHHHHHHh------HH
Confidence 34566788999986 57888888888887653 2111233334556665 99988888888766331 23
Q ss_pred hhhHHHHHHhhccCCc-----------hHHHHHhhCcceeccCc
Q 046450 148 IIPTFDFLKGVFQANG-----------NLVYALKQSIRVVNSDI 180 (392)
Q Consensus 148 l~p~v~fL~~lg~~~~-----------~i~~il~~~P~lL~~s~ 180 (392)
....+.||.++|++.. +....|..+|+.|..++
T Consensus 143 ~~~~~~~L~~~gi~~~~a~ki~~~yg~~~~~~i~~nPY~L~~~i 186 (720)
T TIGR01448 143 ERRLLAGLQGLGIGIKLAQRIYKFYQADTLDRVEKDPYLLAEDV 186 (720)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHhHHHHHHHHhCchhhhhhc
Confidence 5667789999998754 34556778888776543
No 36
>PRK14487 cbb3-type cytochrome c oxidase subunit II; Provisional
Probab=31.28 E-value=1.3e+02 Score=27.37 Aligned_cols=63 Identities=10% Similarity=-0.027 Sum_probs=37.2
Q ss_pred ccccCCceeeechh--hHHHHHHHHHHhCCCCCchhHHHHHHHHHhc-----------CHHHHHHHHHHHHHcCCC
Q 046450 204 LIMLQPPSLVLRAE--LFKNVVDVIKEMGFEPSSKSFILAVRSMAMS-----------SKATWQRKKEILISFGWS 266 (392)
Q Consensus 204 ll~~~P~il~~~~~--~~~~~v~~L~~lG~~~~~~~~~~~~~~~~~~-----------s~~~l~~kv~fL~~lG~s 266 (392)
++-.+|+++....+ .+..++..++.+|++..+.....+...+... ....+..-|.||+++|-.
T Consensus 134 ~MPay~~L~~~~ld~~~~~~~l~~l~~~gvPYt~~~i~~a~~~~~~~a~~~~~~~~~~~~te~~AliAYLq~LG~~ 209 (217)
T PRK14487 134 NMPAYPWLAENDLDGTDTAEKMTALRVVGVPYTDEDIAGAKAAVKGKADPIADDGDPGEITEMDALIAYLQSLGTA 209 (217)
T ss_pred CCCCCcccccccCCHHHHHHHHHHhhhcCCCCCHHHHHHHHHHHHHhhccccccccCCCccHHHHHHHHHHHhccc
Confidence 44556666644443 6778888888889887765554444332211 124456666677766644
No 37
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=30.78 E-value=1.3e+02 Score=23.30 Aligned_cols=20 Identities=15% Similarity=0.235 Sum_probs=7.6
Q ss_pred hHHHhhhhCCCChHHHHHHH
Q 046450 78 SSIQLLTSRGFTKPQIATLI 97 (392)
Q Consensus 78 ~~l~~L~~lGl~~~~i~~ll 97 (392)
.++.+|..+|++.....++.
T Consensus 10 ~~~~~L~~~gl~~~~a~kl~ 29 (94)
T PF14490_consen 10 ELMAFLQEYGLSPKLAMKLY 29 (94)
T ss_dssp HHHHHHHHTT--HHHHHHHH
T ss_pred HHHHHHHHcCCCHHHHHHHH
Confidence 34444444444444333333
No 38
>PF02631 RecX: RecX family; InterPro: IPR003783 RecX is a putative bacterial regulatory protein []. The gene encoding RecX is found downstream of recA, and it is suggested that the RecX protein might be regulator of RecA activity by interaction with the RecA protein or filament [].; GO: 0006282 regulation of DNA repair; PDB: 3DFG_A 3D5L_B 3C1D_B 3E3V_A.
Probab=29.85 E-value=3e+02 Score=22.16 Aligned_cols=107 Identities=14% Similarity=0.090 Sum_probs=0.0
Q ss_pred hhhHHHHHHhhcc-CCchHHHHHhhCcceeccCcccchhhhHHHHHHCCCCchhhhcccccCCceeeechhhHHHHHHHH
Q 046450 148 IIPTFDFLKGVFQ-ANGNLVYALKQSIRVVNSDIQKRVVPNMNTLRAHGVPEPHIARLIMLQPPSLVLRAELFKNVVDVI 226 (392)
Q Consensus 148 l~p~v~fL~~lg~-~~~~i~~il~~~P~lL~~s~~~~l~~~v~~L~~lGv~~~~i~~ll~~~P~il~~~~~~~~~~v~~L 226 (392)
+...+++|.+.|. ++...+....+ .-+.....+ -.....-|+.-|++.+.|...+...+. ...-..-.-..+
T Consensus 11 I~~vi~~l~~~gyidD~~ya~~~v~--~~~~~~~~G-~~~I~~~L~~kGi~~~~i~~~l~~~~~----~e~a~~~~~kk~ 83 (121)
T PF02631_consen 11 IEEVIDRLKELGYIDDERYAESYVR--SRLRRKGKG-PRRIRQKLKQKGIDREIIEEALEEYDE----EEEALELAEKKY 83 (121)
T ss_dssp HHHHHHHHHHTTSS-HHHHHHHHHH--HHHHHTT---HHHHHHHHHHTT--HHHHHHHHTCS-H----HHHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHHH--Hhccccccc-HHHHHHHHHHHCCChHHHHHHHHHhhH----HHHHHHHHHHHH
Q ss_pred HHhCCCCCchhHHHHHHHHHhcCHHHHHHHHHHHHHcCCCHHHHHHHHHh
Q 046450 227 KEMGFEPSSKSFILAVRSMAMSSKATWQRKKEILISFGWSEDEFRMVFKR 276 (392)
Q Consensus 227 ~~lG~~~~~~~~~~~~~~~~~~s~~~l~~kv~fL~~lG~s~~ei~~~i~~ 276 (392)
....-... ....++-+.+|.+-||+.+.|..++..
T Consensus 84 ~~~~~~~~---------------~~~~~K~~~~L~rrGF~~~~i~~vi~~ 118 (121)
T PF02631_consen 84 RRYRKPSD---------------RKRKQKLIRFLMRRGFSYDVIRRVISE 118 (121)
T ss_dssp HHTTTS-C---------------HHHHHHHHHHHHHTT--HHHHHHHCHH
T ss_pred hcccCCCC---------------HHHHHHHHHHHHHCCCCHHHHHHHHhh
No 39
>PF08069 Ribosomal_S13_N: Ribosomal S13/S15 N-terminal domain; InterPro: IPR012606 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This domain is found at the N terminus of ribosomal S13 and S15 proteins. This domain is also identified as NUC021 [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3U5C_N 3O30_G 3IZB_O 3O2Z_G 3U5G_N 2XZN_O 2XZM_O 3IZ6_O.
Probab=29.38 E-value=19 Score=25.77 Aligned_cols=35 Identities=11% Similarity=0.050 Sum_probs=21.9
Q ss_pred HHHHHhcCHHHHHHHHHHHHHcCCCHHHHHHHHHh
Q 046450 242 VRSMAMSSKATWQRKKEILISFGWSEDEFRMVFKR 276 (392)
Q Consensus 242 ~~~~~~~s~~~l~~kv~fL~~lG~s~~ei~~~i~~ 276 (392)
++.-+..+.+.+++.|--|.+-|++..+|.-+++.
T Consensus 22 ~P~W~~~~~~eVe~~I~klakkG~tpSqIG~iLRD 56 (60)
T PF08069_consen 22 PPSWLKYSPEEVEELIVKLAKKGLTPSQIGVILRD 56 (60)
T ss_dssp --TT--S-HHHHHHHHHHHCCTTHCHHHHHHHHHH
T ss_pred CCCCcCCCHHHHHHHHHHHHHcCCCHHHhhhhhhh
Confidence 33334456677777777777788888888877765
No 40
>PHA02591 hypothetical protein; Provisional
Probab=28.74 E-value=81 Score=23.84 Aligned_cols=44 Identities=25% Similarity=0.354 Sum_probs=28.5
Q ss_pred cCCCHHHHHhhcc----cccccCCCChhhHHHhhhhCCCChHHHHHHH
Q 046450 54 CGLSLEKAISVSK----LVKIQDTEKPNSSIQLLTSRGFTKPQIATLI 97 (392)
Q Consensus 54 ~Gls~~~~~~i~~----~~~~~~~~~~~~~l~~L~~lGl~~~~i~~ll 97 (392)
|.++.....+++. ++...+.+++.++..-|.+.|++..+|++.+
T Consensus 22 ~~~~~~~m~k~vqv~~~ryfi~~~dd~~~vA~eL~eqGlSqeqIA~~L 69 (83)
T PHA02591 22 CYIGEKKMQKVVQVGQTRYFVESEDDLISVTHELARKGFTVEKIASLL 69 (83)
T ss_pred EEhhhHhHHHhheeCCEEEEEeccchHHHHHHHHHHcCCCHHHHHHHh
Confidence 4455555555542 2344566777778888888888888777654
No 41
>PF13331 DUF4093: Domain of unknown function (DUF4093)
Probab=26.51 E-value=2.7e+02 Score=21.45 Aligned_cols=22 Identities=23% Similarity=0.412 Sum_probs=12.3
Q ss_pred hhHHHHHHHhCCCCchhHHHhh
Q 046450 112 LKPKIEYLESLGISGPDLAKIL 133 (392)
Q Consensus 112 l~p~v~fL~~lGls~~~l~~il 133 (392)
-..-+..|..+|++.+++..++
T Consensus 65 ~KqllkrLN~f~it~~e~~~al 86 (87)
T PF13331_consen 65 AKQLLKRLNMFGITREEFEEAL 86 (87)
T ss_pred HHHHHHHHHHcCCCHHHHHHHh
Confidence 3444555556666666655543
No 42
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=26.05 E-value=1.1e+02 Score=22.06 Aligned_cols=40 Identities=23% Similarity=0.434 Sum_probs=26.1
Q ss_pred HHCCCCchhhhcccccCCceeeechhhHHHHHHHHHHhCCCCC
Q 046450 192 RAHGVPEPHIARLIMLQPPSLVLRAELFKNVVDVIKEMGFEPS 234 (392)
Q Consensus 192 ~~lGv~~~~i~~ll~~~P~il~~~~~~~~~~v~~L~~lG~~~~ 234 (392)
+.+|++...|.+++...|.+ +++..+...+.++++|+.++
T Consensus 8 ~~~gvS~~TVSr~ln~~~~v---~~~t~~~i~~~~~~~gy~~~ 47 (70)
T smart00354 8 RLAGVSKATVSRVLNGNGRV---SEETREKVLAAMEELGYIPN 47 (70)
T ss_pred HHHCCCHHHHHHHHCCCCCC---CHHHHHHHHHHHHHhCCCCC
Confidence 35788888777777655543 45555666666677777654
No 43
>PF11212 DUF2999: Protein of unknown function (DUF2999); InterPro: IPR021376 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=25.64 E-value=1.1e+02 Score=22.67 Aligned_cols=49 Identities=16% Similarity=0.342 Sum_probs=27.8
Q ss_pred hhHHHHHHhhccCCchHHHHHhhCcceeccCcccchhhhHHHHHHCCCCchhhhccc
Q 046450 149 IPTFDFLKGVFQANGNLVYALKQSIRVVNSDIQKRVVPNMNTLRAHGVPEPHIARLI 205 (392)
Q Consensus 149 ~p~v~fL~~lg~~~~~i~~il~~~P~lL~~s~~~~l~~~v~~L~~lGv~~~~i~~ll 205 (392)
.|.+..|++-.++++.|..++.. |+. |--.......++|++++.+..++
T Consensus 2 NPIia~LKehnvsd~qi~elFq~----lT~----NPl~AMa~i~qLGip~eKLQ~lm 50 (82)
T PF11212_consen 2 NPIIAILKEHNVSDEQINELFQA----LTQ----NPLAAMATIQQLGIPQEKLQQLM 50 (82)
T ss_pred chHHHHHHHcCCCHHHHHHHHHH----Hhh----CHHHHHHHHHHcCCCHHHHHHHH
Confidence 45666777777777766665532 111 12234455566777777655443
No 44
>cd08319 Death_RAIDD Death domain of RIP-associated ICH-1 homologous protein with a death domain. Death domain (DD) of RAIDD (RIP-associated ICH-1 homologous protein with a death domain), also known as CRADD (Caspase and RIP adaptor). RAIDD is an adaptor protein that together with the p53-inducible protein PIDD and caspase-2, forms the PIDDosome complex, which is required for caspase-2 activation and plays a role in mediating stress-induced apoptosis. RAIDD contains an N-terminal Caspase Activation and Recruitment Domain (CARD), which interacts with the caspase-2 CARD, and a C-terminal DD, which interacts with the DD of PIDD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD, DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other pr
Probab=24.58 E-value=3.1e+02 Score=20.88 Aligned_cols=37 Identities=14% Similarity=0.161 Sum_probs=23.5
Q ss_pred HhhhhCCCChHHHHHHHHhCCceeccCcCCchhHHHHHHHh
Q 046450 81 QLLTSRGFTKPQIATLISKYPRILSHDPEKVLKPKIEYLES 121 (392)
Q Consensus 81 ~~L~~lGl~~~~i~~ll~~~P~lL~~~~~~~l~p~v~fL~~ 121 (392)
.+.+.+|++..+|..+-..||.= ....+..-+.-|+.
T Consensus 18 ~Lar~Lgls~~~I~~i~~~~p~~----l~eQv~~mL~~W~~ 54 (83)
T cd08319 18 QVLLDLGLSQTDIYRCKENHPHN----VQSQIVEALVKWRQ 54 (83)
T ss_pred HHHHHcCCCHHHHHHHHHhCCCC----HHHHHHHHHHHHHH
Confidence 34568899999998888888842 22234444544443
No 45
>cd00739 DHPS DHPS subgroup of Pterin binding enzymes. DHPS (dihydropteroate synthase), a functional homodimer, catalyzes the condensation of p-aminobenzoic acid (pABA) in the de novo biosynthesis of folate, which is an essential cofactor in both nucleic acid and protein biosynthesis. Prokaryotes (and some lower eukaryotes) must synthesize folate de novo, while higher eukaryotes are able to utilize dietary folate and therefore lack DHPS. Sulfonamide drugs, which are substrate analogs of pABA, target DHPS.
Probab=24.40 E-value=2.5e+02 Score=26.31 Aligned_cols=69 Identities=9% Similarity=0.120 Sum_probs=42.9
Q ss_pred HHHHHHHHHHhhCCChhhHhcCCcc-cccCCCCccchhHHHHHHHHHcCCCCCCcccccccccChHHHHHHHhccCCCC
Q 046450 288 IRKLMDFFVNKIGLEPSDIARYPNL-LIGSLEKKVLPRWSVLQVLMSKNLLKKDVNVSLALFVTKEVFERRFVTSYMHE 365 (392)
Q Consensus 288 L~~~~~fL~~~~G~~~~~i~~~P~l-L~~sle~~l~pR~~~l~~L~~~G~~~~~~~l~~~l~~s~~~F~~~~v~~~~e~ 365 (392)
++.+++.+.+ .|++.++|.--|-+ +..+ -...+..++.+.... ......++..|.+.|...+....+++
T Consensus 152 ~~~~i~~~~~-~Gi~~~~Ii~DPg~gf~ks----~~~~~~~l~~i~~l~----~~~~pil~G~SrkSfig~~~~~~~~~ 221 (257)
T cd00739 152 LEARLEAAES-AGVARNRIILDPGIGFGKT----PEHNLELLRRLDELK----QLGLPVLVGASRKSFIGALLGREPKD 221 (257)
T ss_pred HHHHHHHHHH-cCCCHHHEEEecCCCcccC----HHHHHHHHHHHHHHH----hCCCcEEEEecccHHHHHhcCCCccc
Confidence 6677788876 89999998877855 3333 122233333222211 11346788999999998887755544
No 46
>PF12244 DUF3606: Protein of unknown function (DUF3606); InterPro: IPR022037 This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 85 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=24.35 E-value=52 Score=23.21 Aligned_cols=29 Identities=14% Similarity=0.173 Sum_probs=23.1
Q ss_pred CCCCCchHHHhHhhcCCCHHHHHhhcccc
Q 046450 40 SDERSPTVSFLTHSCGLSLEKAISVSKLV 68 (392)
Q Consensus 40 ~~~~~~~v~~L~~~~Gls~~~~~~i~~~~ 68 (392)
+-..+..|.|....+|+|++++..++..+
T Consensus 16 ~~~e~~ev~ywa~~~gvt~~~L~~AV~~v 44 (57)
T PF12244_consen 16 DLSEPYEVRYWAKRFGVTEEQLREAVRAV 44 (57)
T ss_pred CCCCHHHHHHHHHHHCcCHHHHHHHHHHH
Confidence 33555678999999999999999987764
No 47
>cd08319 Death_RAIDD Death domain of RIP-associated ICH-1 homologous protein with a death domain. Death domain (DD) of RAIDD (RIP-associated ICH-1 homologous protein with a death domain), also known as CRADD (Caspase and RIP adaptor). RAIDD is an adaptor protein that together with the p53-inducible protein PIDD and caspase-2, forms the PIDDosome complex, which is required for caspase-2 activation and plays a role in mediating stress-induced apoptosis. RAIDD contains an N-terminal Caspase Activation and Recruitment Domain (CARD), which interacts with the caspase-2 CARD, and a C-terminal DD, which interacts with the DD of PIDD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD, DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other pr
Probab=23.94 E-value=2.5e+02 Score=21.40 Aligned_cols=68 Identities=22% Similarity=0.313 Sum_probs=41.2
Q ss_pred hhHHHHH-HHhCCCCchhHHHhhhcCccccccccccchhhHHHHHHhhccCCchHHHHHhhCcceeccCcccchhhhHHH
Q 046450 112 LKPKIEY-LESLGISGPDLAKILCPYPELLSRSLENHIIPTFDFLKGVFQANGNLVYALKQSIRVVNSDIQKRVVPNMNT 190 (392)
Q Consensus 112 l~p~v~f-L~~lGls~~~l~~il~~~P~lL~~~~~~~l~p~v~fL~~lg~~~~~i~~il~~~P~lL~~s~~~~l~~~v~~ 190 (392)
|-+..+- .+.+|++..+|..+-..+|. ++...+...+.-|++-....+ ++..-+..
T Consensus 12 LG~~W~~Lar~Lgls~~~I~~i~~~~p~----~l~eQv~~mL~~W~~r~G~~A-------------------Tv~~L~~a 68 (83)
T cd08319 12 LGPEWEQVLLDLGLSQTDIYRCKENHPH----NVQSQIVEALVKWRQRFGKKA-------------------TVQSLIQS 68 (83)
T ss_pred HhhhHHHHHHHcCCCHHHHHHHHHhCCC----CHHHHHHHHHHHHHHhcCCCC-------------------cHHHHHHH
Confidence 4444443 44799999999999998886 233345555555555322332 24445566
Q ss_pred HHHCCCCchhhh
Q 046450 191 LRAHGVPEPHIA 202 (392)
Q Consensus 191 L~~lGv~~~~i~ 202 (392)
|+.+|+.++...
T Consensus 69 L~~~~~~~~~~~ 80 (83)
T cd08319 69 LKAVEVDPSVLQ 80 (83)
T ss_pred HHHcCCCHHHHH
Confidence 777777665543
No 48
>PF09278 MerR-DNA-bind: MerR, DNA binding; InterPro: IPR015358 This entry represents a family of DNA-binding domains that are predominantly found in the prokaryotic transcriptional regulator MerR. They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold []. ; PDB: 3QAO_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q09_A 1Q08_B 1Q0A_B 1Q07_A ....
Probab=23.69 E-value=79 Score=22.28 Aligned_cols=18 Identities=28% Similarity=0.429 Sum_probs=13.3
Q ss_pred HHHHHHcCCCHHHHHHHH
Q 046450 257 KEILISFGWSEDEFRMVF 274 (392)
Q Consensus 257 v~fL~~lG~s~~ei~~~i 274 (392)
|..++.+|||-+||..++
T Consensus 7 I~~~r~lGfsL~eI~~~l 24 (65)
T PF09278_consen 7 IRRLRELGFSLEEIRELL 24 (65)
T ss_dssp HHHHHHTT--HHHHHHHH
T ss_pred HHHHHHcCCCHHHHHHHH
Confidence 445668999999999999
No 49
>KOG0400 consensus 40S ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=22.78 E-value=91 Score=25.97 Aligned_cols=36 Identities=11% Similarity=0.190 Sum_probs=25.6
Q ss_pred hhCcceeccCcccchhhhHHHHHHCCCCchhhhcccc
Q 046450 170 KQSIRVVNSDIQKRVVPNMNTLRAHGVPEPHIARLIM 206 (392)
Q Consensus 170 ~~~P~lL~~s~~~~l~~~v~~L~~lGv~~~~i~~ll~ 206 (392)
+..|..|..+.++ ++.-|--+..-|+++.+|+-++.
T Consensus 20 r~~PtWlK~~~dd-vkeqI~K~akKGltpsqIGviLR 55 (151)
T KOG0400|consen 20 RSVPTWLKLTADD-VKEQIYKLAKKGLTPSQIGVILR 55 (151)
T ss_pred cCCcHHHhcCHHH-HHHHHHHHHHcCCChhHceeeee
Confidence 4567777777776 77766677777888888876554
No 50
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=22.62 E-value=1.4e+02 Score=26.64 Aligned_cols=26 Identities=19% Similarity=0.259 Sum_probs=21.6
Q ss_pred hhHHHHHHHhCCCCchhHHHhhhcCc
Q 046450 112 LKPKIEYLESLGISGPDLAKILCPYP 137 (392)
Q Consensus 112 l~p~v~fL~~lGls~~~l~~il~~~P 137 (392)
+...+.+|.++|+++.++.+++..+-
T Consensus 149 ~~ev~~aL~~LG~~~~~a~~~~~~~~ 174 (192)
T PRK00116 149 LEEAVSALVALGYKPKEASKAVAKIL 174 (192)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHh
Confidence 67778899999999999888887763
No 51
>cd08306 Death_FADD Fas-associated Death Domain protein-protein interaction domain. Death domain (DD) found in FAS-associated via death domain (FADD). FADD is a component of the death-inducing signaling complex (DISC) and serves as an adaptor in the signaling pathway of death receptor proteins. It modulates apoptosis as well as non-apoptotic processes such as cell cycle progression, survival, innate immune signaling, and hematopoiesis. FADD contains an N-terminal DED and a C-terminal DD. Its DD interacts with the DD of the activated death receptor, FAS, and its DED recruits the initiator caspases, caspase-8 and -10, to the DISC complex via a homotypic interaction with the N-terminal DED of the caspase. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain),
Probab=22.17 E-value=1.5e+02 Score=22.65 Aligned_cols=37 Identities=14% Similarity=0.302 Sum_probs=21.7
Q ss_pred HHhhhhCCCChHHHHHHHHhCCceeccCcCCchhHHHHHHH
Q 046450 80 IQLLTSRGFTKPQIATLISKYPRILSHDPEKVLKPKIEYLE 120 (392)
Q Consensus 80 l~~L~~lGl~~~~i~~ll~~~P~lL~~~~~~~l~p~v~fL~ 120 (392)
-++-+.+|++..+|..+-..+|. +........+..+.
T Consensus 17 k~laR~LGlse~~Id~i~~~~~~----~~~eq~~~mL~~W~ 53 (86)
T cd08306 17 RKLARKLGLSETKIESIEEAHPR----NLREQVRQSLREWK 53 (86)
T ss_pred HHHHHHcCCCHHHHHHHHHHCCC----CHHHHHHHHHHHHH
Confidence 44556777887777777777773 22223445554444
No 52
>TIGR03060 PS_II_psb29 photosystem II biogenesis protein Psp29. Psp29, originally designated sll1414 in Synechocystis 6803, is found universally in Cyanobacteria and in Arabidopsis. It was isolated and partially sequenced from purified photosystem II (PS II) in Synechocystis. While its function is unknown, mutant studies show an impairment in photosystem II biogenesis and/or stability, rather than in PS II core function.
Probab=21.49 E-value=2.8e+02 Score=25.33 Aligned_cols=42 Identities=17% Similarity=0.144 Sum_probs=30.9
Q ss_pred hHHHhHhhcCCCHHHHHhhcccc-cccCCCChhhHHHhhhhCC
Q 046450 46 TVSFLTHSCGLSLEKAISVSKLV-KIQDTEKPNSSIQLLTSRG 87 (392)
Q Consensus 46 ~v~~L~~~~Gls~~~~~~i~~~~-~~~~~~~~~~~l~~L~~lG 87 (392)
-.+.|+.+.|++++++++.+..+ ......+.+....||..-|
T Consensus 76 IF~Alc~a~~~dp~~~r~dA~~l~~~a~~~s~~~i~~~l~~~~ 118 (214)
T TIGR03060 76 LFDALCNSNGFDPEQLREDAKQLLEQAKGKGLDEILSWLTQAN 118 (214)
T ss_pred HHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCHHHHHHHHhccc
Confidence 34889999999999999987764 2333456677788887654
No 53
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=21.21 E-value=1.4e+02 Score=19.75 Aligned_cols=40 Identities=28% Similarity=0.538 Sum_probs=23.4
Q ss_pred HHCCCCchhhhcccccCCceeeechhhHHHHHHHHHHhCCCCC
Q 046450 192 RAHGVPEPHIARLIMLQPPSLVLRAELFKNVVDVIKEMGFEPS 234 (392)
Q Consensus 192 ~~lGv~~~~i~~ll~~~P~il~~~~~~~~~~v~~L~~lG~~~~ 234 (392)
+.+|++...|.+++.-.|. .+.+......+.+.++|+.++
T Consensus 5 ~~~gvs~~tvs~~l~g~~~---vs~~~~~~i~~~~~~l~~~~~ 44 (52)
T cd01392 5 RAAGVSVATVSRVLNGKPR---VSEETRERVLAAAEELGYRPN 44 (52)
T ss_pred HHHCcCHHHHHHHHcCCCC---CCHHHHHHHHHHHHHhCCCCC
Confidence 3567777777776665542 233444555555566676654
No 54
>PF10440 WIYLD: Ubiquitin-binding WIYLD domain; InterPro: IPR018848 This entry represents a presumed domain which has been predicted to contain three alpha helices. It was named the WIYLD domain based on the pattern of the ost conserved residues []. This domain appears to be specific to plant SET-domain proteins. ; GO: 0018024 histone-lysine N-methyltransferase activity
Probab=20.88 E-value=1.8e+02 Score=21.18 Aligned_cols=35 Identities=14% Similarity=0.215 Sum_probs=22.7
Q ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHhCCcccccc
Q 046450 250 KATWQRKKEILISFGWSEDEFRMVFKRQPLFMMAS 284 (392)
Q Consensus 250 ~~~l~~kv~fL~~lG~s~~ei~~~i~~~P~iL~~s 284 (392)
.+.+..-++.++.+||+.++|...+.+-=.+...+
T Consensus 8 ~~R~daA~dam~~lG~~~~~v~~vl~~LL~lY~~n 42 (65)
T PF10440_consen 8 NERIDAALDAMRQLGFSKKQVRPVLKNLLKLYDGN 42 (65)
T ss_pred cHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHcCC
Confidence 34556667777888888888876666543333333
No 55
>PF03960 ArsC: ArsC family; InterPro: IPR006660 Several bacterial taxon have a chromosomal resistance system, encoded by the ars operon, for the detoxification of arsenate, arsenite, and antimonite []. This system transports arsenite and antimonite out of the cell. The pump is composed of two polypeptides, the products of the arsA and arsB genes. This two-subunit enzyme produces resistance to arsenite and antimonite. Arsenate, however, must first be reduced to arsenite before it is extruded. A third gene, arsC, expands the substrate specificity to allow for arsenate pumping and resistance. ArsC is an approximately 150-residue arsenate reductase that uses reduced glutathione (GSH) to convert arsenate to arsenite with a redox active cysteine residue in the active site. ArsC forms an active quaternary complex with GSH, arsenate, and glutaredoxin 1 (Grx1). The three ligands must be present simultaneously for reduction to occur []. The arsC family also comprises the Spx proteins which are GRAM-positive bacterial transcription factors that regulate the transcription of multiple genes in response to disulphide stress []. The arsC protein structure has been solved []. It belongs to the thioredoxin superfamily fold which is defined by a beta-sheet core surrounded by alpha-helices. The active cysteine residue of ArsC is located in the loop between the first beta-strand and the first helix, which is also conserved in the Spx protein and its homologues.; PDB: 2KOK_A 1SK1_A 1SK2_A 1JZW_A 1J9B_A 1S3C_A 1SD8_A 1SD9_A 1I9D_A 1SK0_A ....
Probab=20.72 E-value=86 Score=24.94 Aligned_cols=54 Identities=13% Similarity=0.208 Sum_probs=28.9
Q ss_pred CCCHHHHHhhccccc--ccCC-CChhhHHHh---hhhCCCChHHHHHHHHhCCceeccCc
Q 046450 55 GLSLEKAISVSKLVK--IQDT-EKPNSSIQL---LTSRGFTKPQIATLISKYPRILSHDP 108 (392)
Q Consensus 55 Gls~~~~~~i~~~~~--~~~~-~~~~~~l~~---L~~lGl~~~~i~~ll~~~P~lL~~~~ 108 (392)
++|.+++..+..... .... ++-.....- +....++.+++..++..+|.++...+
T Consensus 32 p~s~~el~~~l~~~~~~~~~lin~~~~~~k~l~~~~~~~~s~~e~i~~l~~~p~LikRPI 91 (110)
T PF03960_consen 32 PLSREELRELLSKLGNGPDDLINTRSKTYKELGKLKKDDLSDEELIELLLENPKLIKRPI 91 (110)
T ss_dssp ---HHHHHHHHHHHTSSGGGGB-TTSHHHHHTTHHHCTTSBHHHHHHHHHHSGGGB-SSE
T ss_pred CCCHHHHHHHHHHhcccHHHHhcCccchHhhhhhhhhhhhhhHHHHHHHHhChhheeCCE
Confidence 566777777665432 1110 011111222 22356889999999999999987763
No 56
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=20.39 E-value=2.7e+02 Score=22.74 Aligned_cols=22 Identities=23% Similarity=0.088 Sum_probs=18.1
Q ss_pred HHHHHHHHcCCCHHHHHHHHHh
Q 046450 255 RKKEILISFGWSEDEFRMVFKR 276 (392)
Q Consensus 255 ~kv~fL~~lG~s~~ei~~~i~~ 276 (392)
..+..++.+|||-++|..++..
T Consensus 48 ~~I~~lr~~G~sL~eI~~~l~~ 69 (127)
T cd04784 48 LFIRRCRSLDMSLDEIRTLLQL 69 (127)
T ss_pred HHHHHHHHcCCCHHHHHHHHHh
Confidence 4567788999999999998863
No 57
>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription]
Probab=20.34 E-value=97 Score=27.00 Aligned_cols=28 Identities=11% Similarity=0.395 Sum_probs=15.4
Q ss_pred HHhCCccccccHHHHHHHHHHHHHhhCCC
Q 046450 274 FKRQPLFMMASAKKIRKLMDFFVNKIGLE 302 (392)
Q Consensus 274 i~~~P~iL~~s~e~L~~~~~fL~~~~G~~ 302 (392)
+...|-+...+.+++...++...+ .|++
T Consensus 70 iM~spvv~v~pdDsi~~vv~lM~~-~g~S 97 (187)
T COG3620 70 IMHSPVVSVSPDDSISDVVNLMRD-KGIS 97 (187)
T ss_pred hccCCeeEECchhhHHHHHHHHHH-cCCc
Confidence 344454444444566666666665 4655
No 58
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=20.26 E-value=2.1e+02 Score=22.19 Aligned_cols=24 Identities=17% Similarity=0.225 Sum_probs=19.7
Q ss_pred HHHHHHHHcCCCHHHHHHHHHhCC
Q 046450 255 RKKEILISFGWSEDEFRMVFKRQP 278 (392)
Q Consensus 255 ~kv~fL~~lG~s~~ei~~~i~~~P 278 (392)
..+.+|+.+|++-++|..++....
T Consensus 48 ~~I~~lr~~G~~l~~I~~~l~~~~ 71 (96)
T cd04768 48 QFILFLRELGFSLAEIKELLDTEM 71 (96)
T ss_pred HHHHHHHHcCCCHHHHHHHHhcCc
Confidence 356778899999999999987654
No 59
>KOG0400 consensus 40S ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=20.09 E-value=88 Score=26.07 Aligned_cols=68 Identities=10% Similarity=0.107 Sum_probs=34.2
Q ss_pred chhHHHHHHHHHhcCHHHHHHHHHHHHHcCCCHHHHHHHHHhCCccccccHHHHHHHHHHHHHhhCCCh
Q 046450 235 SKSFILAVRSMAMSSKATWQRKKEILISFGWSEDEFRMVFKRQPLFMMASAKKIRKLMDFFVNKIGLEP 303 (392)
Q Consensus 235 ~~~~~~~~~~~~~~s~~~l~~kv~fL~~lG~s~~ei~~~i~~~P~iL~~s~e~L~~~~~fL~~~~G~~~ 303 (392)
...+.++++.-+..+.+.+++.+--|.+-|++..||.-+++..=.|=.++.-.=...+.+|.. -|+-+
T Consensus 15 AlPY~r~~PtWlK~~~ddvkeqI~K~akKGltpsqIGviLRDshGi~q~r~v~G~kI~Rilk~-~Gl~P 82 (151)
T KOG0400|consen 15 ALPYRRSVPTWLKLTADDVKEQIYKLAKKGLTPSQIGVILRDSHGIGQVRFVTGNKILRILKS-NGLAP 82 (151)
T ss_pred ccccccCCcHHHhcCHHHHHHHHHHHHHcCCChhHceeeeecccCcchhheechhHHHHHHHH-cCCCC
Confidence 334444445445556666666666666667777776655444333222222112223445544 56653
No 60
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=20.06 E-value=2.9e+02 Score=21.39 Aligned_cols=24 Identities=17% Similarity=0.166 Sum_probs=19.7
Q ss_pred HHHHHHHHcCCCHHHHHHHHHhCC
Q 046450 255 RKKEILISFGWSEDEFRMVFKRQP 278 (392)
Q Consensus 255 ~kv~fL~~lG~s~~ei~~~i~~~P 278 (392)
..+..++++|++-++|..++....
T Consensus 48 ~~I~~lr~~G~~l~eI~~~l~~~~ 71 (96)
T cd04788 48 HQIIALRRLGFSLREIGRALDGPD 71 (96)
T ss_pred HHHHHHHHcCCCHHHHHHHHhCCC
Confidence 456778899999999999987654
Done!